When I am driving and step on the brake to stop, the brake peddle feels like it is thumping or popping. What can this be?

do you know what the codes are that are coming up? and it sounds like there is some thing loose. a motor mount or a transmission mount

My thought would be to look at the u joints and drive line. When driving the car and it makes the thumbing sound shift to natural, if the sound stops it is probably in drive line.

If it's a vibration, it might be a brake pad staying in contact with the disk. Normally the pads push away when the car starts moving. (A normal condition called "runout") Try stopping your Jeep tonite by using only rear brakes. (hand brake) Don't step on the brake pedal at all. Then see if it does it in the morning. Don't step on the brake pedal in the morning till the test 20 sec's is over.

If the problem is a thump thump sound it's probably a tire flat spot from setting. Have the tires just been replaced? Could be a softer tirs material.

Sounds like you have warped rotors and or a lose caliper mounting bolt . When you stop do you feel a vibration in the brake peddle or in the steering wheel or both ? IF you feel the pulsation in the brake peddle I would suspect a brake pad / brake rotor problem . Now if you do not feel it in either and the vibration is through the whole car with out the brakes being applied i would think it may be related to and engine/drive line problem (motor mount /trans mount /axle problem)

Sounds like you will have to bleed your brakes again, but thats not the problem og hard brake peddle, need to check your power brake booster, sit right in back of master cylinder, check make sure it has vacum going to it, also to test it with engine off, press on brake peddle three time, then state engine with foot on peddle, peddle should go down a few inches, also with engine of peddle should feel soft for three pumps, if you have none of this , power brake booster is bad.

well maybe the lines are not bleed right. did you bleed the master??

that is one of the wosrt ABS system it dose cause a soft peddle but you can sometimes adjust up the rear brakes to help this problem,also find a dirt road and slam on the brakes just enough to cause the ABS pump to kick on it will also give you a better peddle

sounds like your servo is at fault try bleeding all 4 wheels with engine running right wheel warped disc

If you can feel it in the brake peddle when you push on it, then your brake rotors are warped. Putting new pads and rotors in will solve this. Is caused by braking too hard (driving really fast to a stop sign and stopping in the last few feet). I have heard a few times that some people upgrade to a better brake when they increase wheel size, but I do not think that is a problem in you case.