I have an odd break problem in my 4runner. I thought it was the master cylinder, so i replaced it. The pedal was still really weak, and while bleeding the breaks, pumping the breaks made the motor start skipping and then it shut off. Anyone know what could be wrong?

Sounds like your power brake booster needs replacement. It uses engine vacuum when you step on the brakes so it may have a vacuum leak which makes the engine run lean and rough.