I'm almost positive I indexed it correctly. THe first time I tried to start it a few weeks ago it wouldn't even start because I had it 180deg off. IIRC its not exactly where it should be but as close to the five o'clock as I could get it. I set it a tooth off either way and both were wayyyyy off. I'll try the pin. It always seems like you have to start putting it in with the rotor pointing before the five position for it to hit the five once its dropped in.
I also replaced the CPS on the bellhousing as the old one's had hit exhaust at some point and melted.
I saw another thread on here with similar problems, but his was more TPS related and then he did a full reset on his PCM and it fixed it. I did a full reset (ie + to - for 30 sec, key on, headlights on/off, key off) and it didnt change anything. Actually it made it worse because as I was going to a party last night it started backfiring THROUGH THE INTAKE MANIFOLD when ever it was revved off idle. That stopped when I cut the engine and restarted it

like the PCM was like "oh sorry about that." As I was leaving the party it did it again and went away as soon as I restarted the Jeep.
EDIT: Just pulled new code, a 42 "Fuel pump relay control circuit: A shorted or open condition detected in the fuel pump relay circuit" I saw the fuel level go full and to zero a couple times, but it used to do that all the time unti I had Jeep perform that recall on it just last summer...
EDITEDIT: Just read a 42 can also be ASD relay but since the fuel gauge was reading funny I think its the fuel pump relay circuit