Spongy brakes when i was bleeding the brakes, i heard air coming from the master cylinder reservoir cap. do you think its just the cap, the master cylinder, or the brake power booster.

did you bleed the rear wheels or just the front
air still in the system possibly in the master cylinder

Bad master cylinder . What are you using a scan tool for ? No need Unless your Installing a new Electro-Hydraulic Control Unit (EHCU) or new Brake Pressure Modulator Valve (BPMV).
Hydraulic Brake System Bleeding (Manual)
Caution: Refer to Brake Fluid Irritant Caution in the Preface section.
Notice: Refer to Brake Fluid Effects on Paint and Electrical Components Notice in the Preface section.
Place a clean shop cloth beneath the brake master cylinder to prevent brake fluid spills.
With the ignition OFF and the brakes cool, apply the brakes 3-5 times, or until the brake pedal effort increases significantly, in order to deplete the brake booster power reserve.
If you have performed a brake master cylinder bench bleeding on this vehicle, or if you disconnected the brake pipes from the master cylinder, you must perform the following steps:
3.1. Ensure that the brake master cylinder reservoir is full to the maximum-fill level. If necessary add GM approved brake fluid from a clean, sealed brake fluid container. Refer to Fluid and Lubricant Recommendations.
If removal of the reservoir cap and diaphragm is necessary, clean the outside of the reservoir on and around the cap prior to removal.
3.2. With the rear brake pipe installed securely to the master cylinder, loosen and separate the front brake pipe from the front port of the brake master cylinder.
3.3. Allow a small amount of brake fluid to gravity bleed from the open port of the master cylinder.
3.4. Reconnect the brake pipe to the master cylinder port and tighten securely.
3.5. Have an assistant slowly depress the brake pedal fully and maintain steady pressure on the pedal.
3.6. Loosen the same brake pipe to purge air from the open port of the master cylinder.
3.7. Tighten the brake pipe, then have the assistant slowly release the brake pedal.
3.8. Wait 15 seconds, then repeat steps 3.3-3.7 until all air is purged from the same port of the master cylinder.
3.9. With the front brake pipe installed securely to the master cylinder, after all air has been purged from the front port of the master cylinder, loosen and separate the rear brake pipe from the master cylinder, then repeat steps 3.3-3.8.
3.10. After completing the final master cylinder port bleeding procedure, ensure that both of the brake pipe-to-master cylinder fittings are properly tightened.
Fill the brake master cylinder reservoir with GM approved brake fluid from a clean, sealed brake fluid container. Ensure that the brake master cylinder reservoir remains at least half-full during this bleeding procedure. Add fluid as needed to maintain the proper level.
Clean the outside of the reservoir on and around the reservoir cap prior to removing the cap and diaphragm.
Install a proper box-end wrench onto the RIGHT REAR wheel hydraulic circuit bleeder valve.
Install a transparent hose over the end of the bleeder valve.
Submerge the open end of the transparent hose into a transparent container partially filled with GM approved brake fluid from a clean, sealed brake fluid container.
Have an assistant slowly depress the brake pedal fully and maintain steady pressure on the pedal.
Loosen the bleeder valve to purge air from the wheel hydraulic circuit.
Tighten the bleeder valve, then have the assistant slowly release the brake pedal.
Wait 15 seconds, then repeat steps 8-10 until all air is purged from the same wheel hydraulic circuit.
With the right rear wheel hydraulic circuit bleeder valve tightened securely, after all air has been purged from the right rear hydraulic circuit install a proper box-end wrench onto the LEFT REAR wheel hydraulic circuit bleeder valve.
Install a transparent hose over the end of the bleeder valve, then repeat steps 7-11.
With the left rear wheel hydraulic circuit bleeder valve tightened securely, after all air purged from the left rear hydraulic circuit, install a proper box-end wrench onto the RIGHT FRONT wheel hydraulic circuit bleeder valve.
Install a transparent hose over the end of the bleeder valve, then repeat steps 7-11.
With the right front wheel hydraulic circuit bleeder valve tightened securely, after all air has been purged from the right front hydraulic circuit, install a proper box-end wrench onto the LEFT FRONT wheel hydraulic circuit bleeder valve.
Install a transparent hose over the end of the bleeder valve, then repeat steps 7-11.
After completing the final wheel hydraulic circuit bleeding procedure, ensure that each of the 4 wheel hydraulic circuit bleeder valves are properly tightened.
Fill the brake master cylinder reservoir to the maximum-fill level with GM approved brake fluid from a clean, sealed brake fluid container.
Slowly depress and release the brake pedal. Observe the feel of the brake pedal.
If the brake pedal feels spongy, repeat the bleeding procedure again. If the brake pedal still feels spongy after repeating the bleeding procedure, perform the following steps:
21.1. Inspect the brake system for external leaks. Refer to Brake System External Leak Inspection.
21.2. Pressure bleed the hydraulic brake system in order to purge any air that may still be trapped in the system.
Turn the ignition key ON, with the engine OFF. Check to see if the brake system warning lamp remains illuminated.
Important: If the brake system warning lamp remains illuminated, DO NOT allow the vehicle to be driven until it is diagnosed and repaired.
If the brake system warning lamp remains illuminated, refer to Symptoms - Hydraulic Brakes

If the master cylinder is replaced, care must be taken to prime the new master cylinder by removing all of the air and completely filling it with brake fluid. The spongy feeling is air that is still in the circuits. You will need to bleed the back brakes as well as the front ones again. The order that you bled them seems correct, but perhaps there remained some air in the main trunk lines.

For the best results 2 people are needed. Start at the further distance wheel cylinder and bleed at least three (3) master cylinder reservoir volumes of fluid (back brakes). Bleed the fluid with use of a piece of tubing attached to the bleed port that is long enough to reach almost to the bottom of a long neck or tall clear jar (clear drink bottle works well). When the bleeding begins, after one or two brake pedal pushes, make sure that the end of the tubing is below the surface of the fluid and keep it under. It best to have a clear bleed line (to observe air). Keep pumping the brake pedal while being careful to not completely empty the master cylinder reservoir (leave 1/4 full always). Repeat the same technique for each wheel cylinder with at least two (2) reservoirs full for front brakes. Partially close the bleed ports when almost finished (at least 5 pedal strokes without exit of any air). Completely close the ports during the down stroke of the brake pedal, with the tubing still attached. Be sure each bleed port is closed snuggly.
Most of the brake fluid can be reused, but not the darker portion at the bottom of the jar.

GRAVITY BLEEDING CLUTCH HYDRAULIC CIRCUIT

1. Verify fluid level in brake master cylinder. Top off with DOT 3 brake fluid as necessary. Leave cap off.

2. Raise vehicle on hoist.

3. Remove bleed port protective cap and install suitable size and length of clear hose (4) to monitor and divert fluid into suitable container.

4. Open up the bleed circuit by turning the thumb screw (3) counter clockwise this will start the air purge and fluid fill process.

5. Lower vehicle, but only enough to gain access to and fill the brake master cylinder. NOTE: Do not allow clutch master cylinder to run dry while fluid exits bleed port.

6. Top off brake master cylinder fluid level while air is purged and fluid drains from bleed port. Continue this until no air bubbles are seen and a solid column of fluid exists.

7. Close hydraulic bleed circuit, remove drain hose and replace dust cap on bleed port.

8. From driver's seat, actuate clutch pedal 60-100 times.

9. Apply parking brake. Start engine and verify clutch operation and pedal feel. If pedal feels fine and clutch operates as designed, stop here. If pedal still feels spongy or clutch does not fully disengage, excessive air is still trapped within the system, most likely at the master cylinder.

10. Top off brake master cylinder fluid level with DOT 3 brake fluid as necessary.

POWER BLEEDING CLUTCH HYDRAULIC CIRCUIT

1. Remove reservoir cap and connect bleeder cap to reservoir. NOTE: Use Bleeder Cap/Modified reservoir cap adapter Snap-on #901-059 or equivalent.

2. Connect service filling machine to bleeder cap. NOTE: Use Service Filling Machine/Brake power bleeder Brake power bleeder or equivalent.

3. Service filling machine should be pressurized to at least 2.5 bar (36 PSI).

4. Remove dust cap from bleeder valve and connect the transparent bleeder hose to bleeder valve.

5. Place the other end of hose in the bleeder container to capture the used fluid. The end of the hose MUST be submerged in the DOT 3 brake fluid.

NOTE: Use Bleeder Container To capture hydraulic fluid and Transparent Bleeder Hose To route fluid to container.

6. Turn on the service filling machine.

7. Crack open the bleeder valve (3).

8. Allow fluid to flow out of bleed port until no more air bubbles can be seen in the transparent bleeder hose.

9. Once fluid is free of air bubbles; make 15 quick actuations between clutch pedal stop positions.

10. Close the bleeder valve and disconnect the service filling machine.

11. To remove remaining air, actuate pedal 10 times slowly between pedal stop positions.

12. Check clutch pedal to see if vehicle is properly bled.

13. If vehicle is not properly bled, repeat procedure.

14. Remove bleeder cap from reservoir and replace reservoir cap.

15. Disconnect transparent bleeder hose from bleeder valve and replace dust cap.

Hi there:
I suggest to check this procedure, when the hydraulic brake system must be bled whenever a fluid line has been disconnected because air gets into the system.

A leak in the system may sometimes be indicated by a spongy brake pedal. Air trapped in the system is compressible and does not permit the pressure applied to the brake pedal to be transmitted solidly through the brakes. The system must be absolutely free from air at all times. If the master cylinder has been overhauled or a new cylinder has been installed, bleed the cylinder on a bench before installation. When bleeding brakes, bleed at the wheel most distant from the master cylinder first, the next most distant second, and so on. During the bleeding operation the master cylinder must be kept at least 3 / 4 full of brake fluid.


The ABS bleeding procedure is different from the conventional method. It consists of the following three steps:
Step 1: Conventional manual brake bleed.
Step 2: Bleeding the system using the DRB scan tool.
Step 3: An additional conventional manual brake bleed.

The recommended ABS bleeding procedure is as follows:

1. To bleed the brakes, first carefully clean all dirt from around the master cylinder filler cap. Remove the filler cap and fill the master cylinder with DOT 3 brake fluid to the lower edge of the filler neck.
2. Bleed the master cylinder first. Have a helper operate the brake pedal while bleeding each master cylinder fluid outlet line. Do not allow the master cylinder to to run out of fluid,as this will allow additional air to be drawn into the cylinder.
3. Bleed the brake system in the following sequence:
   1. Master cylinder
   2. HCU valve body (at fluid lines)
   3. Right rear wheel
   4. Left rear wheel
   5. Right front wheel
   6. Left front wheel
4. Clean off the bleeder connections at all four wheel cylinders. Attach the bleeder hose to the right rear wheel cylinder bleeder screw and place the end of the tube in a glass jar, submerged in brake fluid.
5. Open the bleeder valve 1/2 - 3/4 of a turn.
6. Have an assistant depress the brake pedal slowly and allow it to return. Continue this pumping action to force any air out of the system. When bubbles cease to appear at the end of the bleeder hose, close the bleeder valve and remove the hose.
7. Check the level of fluid in the master cylinder reservoir and replenish as necessary.
8. After the bleeding operation at each wheel cylinder has been completed, fill the master cylinder reservoir and replace the filler plug.

Do not reuse the fluid which has been removed from the lines through the bleeding process because it contains air bubbles and dirt.

1. Perform the "Bleed Brake'' procedure with the DRB II scan tool. This procedure is described in the DRB II software information and diagnostic guide.
   1. Attach the DRB II scan tool to the diagnostic connector.
   2. Run the Bleed Brake procedure as described in the DRB II tester guide.
2. Repeat the conventional bleeding procedure as previously outlined.
3. Fill the master cylinder reservoir to the proper level.
4. Check the brake operation.

Hope this helps.

I recommend bleeding the clutch using instructions pasted from autozone.com below. As for the engine light, please get the computer scanned and send us the diagnostic trouble code.
Hydraulic System Bleeding NOTE
It is necessary to bleed the clutch hydraulic release system if the system has lost an excessive amount of fluid and has allowed air into the circuit. Air in the system typically results in a spongy pedal feel, and/or improper clutch release. If air cannot be removed from the system using this procedure, it is necessary to replace both the clutch master cylinder and slave cylinder assemblies.

Except Turbocharged Models

1. From driver's seat, actuate clutch pedal 60-100 times. Verify clutch operation/pedal feel. If pedal still feels spongy, or clutch does not fully disengage, excessive air is still trapped within the system. Perform the following procedure:
2. Verify fluid level in clutch master cylinder reservoir. Top off with DOT 3 brake fluid as necessary.
3. Raise and safely support the vehicle.
4. Remove clutch slave cylinder assembly from the transaxle case, but do not disconnect from the system. Allow the slave cylinder hang, making it the lowest part of the system.
   CAUTION
   While slave cylinder is detached from the transaxle, DO NOT actuate the clutch master cylinder. Damage to the slave cylinder will result.
   
5. Depress slave cylinder pushrod until it bottoms and then release. Repeat this at least ten times, forcing trapped air upwards and out of the system.
6. Re-install slave cylinder into position. Torque slave cylinder to case bolt to 168 inch lbs. (19 Nm).
7. Carefully lower the vehicle.
8. Check and adjust clutch master cylinder fluid level. Actuate clutch pedal thirty (30) times. Verify clutch operation/pedal feel. If pedal still feels spongy, or clutch does not fully disengage, air is still trapped within the system. Repeat Step 3 through Step 7 until air is purged. If several attempts at purging air from the system are unsuccessful, replace both the clutch master cylinder and slave cylinder assemblies.
9. Raise and safely support the vehicle.
10. Carefully lower the vehicle.
11. Top off clutch master cylinder fluid level with DOT 3 brake fluid as necessary.

Turbocharged Models

NOTE
Due to the angle and design of the turbo hydraulic system components, gravity and pedal bleeding are less effective and less efficient than the reverse fluid injection method (reverse bleeding). Reverse bleeding is recommended for this system, and requires the use of commercially available injection bleeding equipment.

Alternate Procedure (Pedal Bleeding)

1. Remove reservoir cap and inspect fluid level. Top off with DOT 3 Brake Fluid. Actuate clutch pedal briskly at least 50 times. Verify release system function. Repeat. If release system is still inoperative, continue with procedure.
2. Raise and safely support the vehicle.
3. Remove clutch bellhousing access cap to expose system bleed screw.
   WARNING
   Use care not to allow fluid to drain into clutch bellhousing. Excessive fluid will be agitated and sprayed around inside the clutch bellhousing by the rotating flywheel, contaminating the flywheel, disc, and pressure plate, resulting in poor clutch engagement.
   
4. Using suitable socket/wrench, loosen bleed screw. Immediately install rubber hose to bleed screw to prevent fluid from entering clutch bellhousing. Tighten bleed screw gently with suitable wrench.
5. Lower vehicle.
6. Have helper actuate clutch pedal to floor.
7. Place collection container at end of hose to capture expelled fluid.
8. Using suitable wrench, break bleeder screw loose and tighten to 62 inch lbs. (7 Nm). Do not over-tighten.
9. Have helper release pedal, returning it to at-rest position, and then actuate pedal to floor.
10. Break bleeder screw loose and tighten to 62 inch lbs. (7 Nm). Do not over-tighten.
11. Repeat procedure as necessary, keeping master cylinder reservoir full during the process, until air bubbles are no longer visible in collection container.
12. When air bubbles are no longer visible, actuate clutch pedal briskly at least 50 times.
13. Verify release system function and top off fluid as necessary.

Recommended Procedure (Reverse Bleeding)

1. Remove reservoir cap and inspect fluid level. Top off with DOT 3 Brake Fluid. Actuate clutch pedal briskly at least 50 times. Verify release system function. Repeat. If release system is still inoperative, continue with procedure.
2. Remove reservoir from bracket and empty into collection container.
3. Raise and safely support the vehicle.
4. Remove clutch bellhousing access cap to expose system bleed screw.
   CAUTION
   Use care not to allow fluid to drain into clutch bellhousing. Excessive fluid will be agitated and sprayed around inside the clutch bellhousing by the rotating flywheel, contaminating the flywheel, disc, and pressure plate, resulting in poor clutch engagement.
   
5. Using suitable socket/wrench, loosen bleed screw.
   
   
   Fig. Location of the bleed screw for the 2.4L engine
   
6. Quickly attach hand operated bleed apparatus to bleed screw. Use care not to over-fill reservoir and spill fluid into engine compartment.
7. Operate bleed gun sufficiently to expel air upward through circuit and out of master cylinder reservoir. Fill and empty reservoir three times.
8. Remove bleed apparatus and tighten bleed screw to 62 inch lbs. (7 Nm). Do not over-tighten.
9. Carefully lower the vehicle.
10. Top off reservoir with fluid, then return the cap.
11. Verify system operation. Actuate clutch pedal 50 times. If necessary, repeat procedure until road test confirms that shift issues no longer exist.

There is still air, presuming all brakes are in good shape and adjusted correctly. One issue is master cylinder PRE BLEEDING. If you do not pre bleed the cylinder, you may never get all of the air out. Parts stores sell a kit that has flexible hoses that connect to the brake line connections and submerge the other ends in the MC reservoir, bleed until no bubbles and from that point DO NOT let the fluid get low in the MC, or start over again.
Doc

Bleeding the Brake System
When any part of the hydraulic system has been disconnected for repair or
replacement, air may get into the lines and cause spongy pedal action (because
air can be compressed and brake fluid cannot). To correct this condition, it is
necessary to bleed the hydraulic system so to be sure all air is purged.

When bleeding the brake system, bleed one brake cylinder at a time, beginning
at the cylinder with the longest hydraulic line (farthest from the master
cylinder) first. ALWAYS Keep the master cylinder reservoir filled with brake
fluid during the bleeding operation. Never use brake fluid that has been drained
from the hydraulic system, no matter how clean it is.

The primary and secondary hydraulic brake systems are separate and are bled
independently. During the bleeding operation, do not allow the reservoir to run
dry. Keep the master cylinder reservoir filled with brake fluid.

1. Clean all dirt from around the master cylinder fill cap, remove the cap and
   fill the master cylinder with brake fluid until the level is within 1/4 I n.
   (6mm) of the top edge of the reservoir.
   
2. Clean the bleeder screws at all 4 wheels. The bleeder screws are located on
   the top of the brake calipers.
   
3. Attach a length of rubber hose over the bleeder screw and place the other
   end of the hose in a glass jar, submerged in brake fluid.
   
4. Starting at the right rear proceed in this order left front, left rear and
   right front.
   
5. Open the bleeder screw 1/2 - 3/4 turn. Have an assistant slowly depress the
   brake pedal.
   
6. Close the bleeder screw and tell your assistant to allow the brake pedal to
   return slowly. Continue this process to purge all air from the system.
   
7. When bubbles cease to appear at the end of the bleeder hose, close the
   bleeder screw and remove the hose.
   
8. Check the master cylinder fluid level and add fluid accordingly. Do this
   after bleeding each wheel.
   
9. Fill the master cylinder reservoir to the proper level.

a Master rates about a 5 out of 10 with 10 being the hardest

you may find the hardest part is the actual bench bleeding of the master
and/or
the replacement of the reservoir

These are the instructions from my service manual, but I do not remove the fluid prior to service steps 2-6

1. Disconnect battery ground cable. Disconnect electrical connector from filler cap.
2. Remove fluid reservoir filler cap.
3. Raise and support vehicle.
4. Remove front wheels.
5. Remove dust cap and loosen bleed nipple. Connect a bleed tube to bleed nipple and into a suitable container.
6. Pump brake pedal until all fluid is expelled. Tighten bleed nipple.
7. Lower vehicle. Install brake fluid reservoir cap. Remove air cleaner and air cleaner outlet tube.
8. Disconnect central electrical box electrical connector.
9. Remove central electrical box retaining screw.
10. Remove central electrical box and relocate to air cleaner area.
11. Disconnect brake fluid feed tube. Disconnect brake lines.
12. On models with anti-lock brakes, disconnect brake lines from Hydraulic Control Unit.
13. On all models, remove brake booster vacuum hose.
14. Extract master cylinder from vehicle.
15. On models with manual transaxles, remove clutch hose from brake/clutch reservoir.
16. On all models, remove master cylinder nuts and remove master cylinder.

To install, reverse removal procedure. Bleed brake system.

it would sound like your master cylinder if you did bleed your brakes right.