1994 XJ intermittent misfire/poor idle on startup

My 1994 Jeep Cherokee Sport idles poorly for about a minute after starting in the morning. While driving it feels like I'm getting kicked in the rear. Sometimes it does it and sometimes not. The motor was rebuilt about 2000 miles ago (according to previous owner) the head has definately been reworked. Check engine light comes on and clears after restarting. Codes present are 12 and 41. Alternator is working normally 14.4 volts. TPS reads .7 volts and moves smoothly to 3.7 volts at WOT. I'm thinking O2 sensor reading incorrectly causing lean F/A mixture. Idk so any help would appreciated. All grounds and connections are good, clean, and tight. Wires and plugs look new. Cap and rotor were cleaned with no effect. Help...

I pulled the plugs and brought the engine to #1 TDC compression, to check distributor position & timing. Appears correct. Cylinders look scarred, parallel rings instead of cross hatch, some vertical scarring. I think the engine was overheated and locked up. The bottom was freed up, but the head was removed and (repaired). Could there be a problem with the valve job causing this aka bent/burned valve that acts up intermittently before taking a dump? Engine has great power when running correctly. Backfired in intake several times when releasing throttle after restarting, then ran fine.

???

Any suggestions are appreciated, I replaced the TPS with no effect. It is now doing it when cold then intermittently after it warms up. I removed all grounds and cleaned with no effect. Codes are 12 and 41.

Bad alternator, charges fine but rectifier is shot. A/C voltage does bad things to Jeeps.