I am installing rear brakes on 1997 lincon mark 8 and cant depress brake cylinders

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

The leak could be due to a leaking brake line in the rear or a leaking brake cylinder. Have the car inspected for the leak by a reputable garage. The car will need to be towed, since it has no brakes.
If you do your own work, refill the master cylinder. Have someone depress the brake peddle while you look under the car for the leak.

Have you tried to bleed the brakes,it sounds like you have air in the system. I would try bleeding the brakes first ,start with the wheel farthest from the master cyl. The right rear,left rear,right front left front. If that does'nt help check the master cyl and brake booster.

1. Check the fluid level in the reservoir after bleeding each wheel. Add DOT3 fluid, if necessary.
2. If the master cylinder was disassembled or if the reservoir becomes empty, bleed the air from the master cylinder as follows:
   1. Disconnect the brake lines from the master cylinder.
   2. Slowly depress the brake pedal and hold it.
   3. Block off the outlet plug with your finger, and release the brake pedal.
   4. Repeat 3 or 4 times.
   
   
3. Bleed the brake starting with the one furthest from the reservoir and then the next furthest, etc.
   
4. Depress the brake pedal several times, then loosen the bleeder plug with the pedal held down.
5. At the point when fluid stops coming out, tighten the bleeder plug to 11 Nm (8 ft. lbs.), then release the brake pedal.
6. Repeat until all the air in the fluid has been bled out.
7. Repeat the procedure to bleed the air out of brake line for each wheel.
8. Check the fluid level and add DOT3 fluid if necessary.

you may have to run the motor as you bleed the brakes so the abs hydraulic unit can purge any air that might be caught within the unit itself.did you bench bleed the master cylinder before installing it on the car.this can save time and reduce the possible chance of air entering the system.make sure you don`t allow the master cylinder to run low on brake fluid.i also assume that you are bleeding the brakes properly.Left front brake works with Right rear brake and Right front brake works with Left rear brake.this is how the brakes should be bleed.

brakes on my Mark 8 have become hard as the brake pedal takes longer to come to a stop and there is a hissing sound. I presume that is the master cylinder power assist..What would that cost to replace parts and labor..

1. Step 1 Mark the brake lines coming into and out of the master cylinder using masking tape and permanent marker.
   
2. Step 2 Orient the tube wrench so that it grabs the end of the nut by first sliding it over the brake line.
   
3. Step 3 Pull the brake lines out of the master cylinder.
   
4. Step 4 Unbolt the two bolts that hold the master cylinder to the brake booster.
   
5. Step 5 Slide the master cylinder off the brake booster.
   
6. Step 6 Remove the bolts that hold the brake booster to the firewall.
   
7. Step 7 Remove the cotter pin from the pin holding the back of the brake pedal to the master cylinder.
   
8. Step 8 Slide the brake booster to brake pedal pin out of the mounting bracket.
   
9. Step 9 Pull the brake booster off the firewall.
   
10. Step 10 Install the new brake booster. Installation is the reverse of removal.
    

disc brakes on the rear of a vehicle have a screw out mechanism that attaches to the ebrake . this means that you must turn the caliper piston to recess into the cylinder.
open the bleed screw to make it move eazier.

bleed the brake again. if the pedal goes to the floor with little resistance, then the master cylinder is your problem.
the shim is to depress the noise when you applied the brake. you can skip that, if the brake works without it.

probably need to be bled again on that side