Got it figured out, thought I would let everyone know about my stupid mistake. First, I changed the MC out, took the TJ out for a drive, the pedal would still go the floor occasionally. I started doing circles in the cul-de-sac in front of my house (yeah, my neighbors were watching me) and realized that when I made a right hand turn, the brakes would go out, but not a left hand turn. I pondered that for a few hours when I realized I should take a look at the front brakes with the steering wheel turned. Sure enough, I noticed a shiny ding on my new shocks, the caliper was hitting it.
I just put in a HP30 that the previous owner had modified the shock mounts by moving them down. Looked like a good idea, but now I have four washers in my left steering stop to compensate.
