98 4.0 liter run problem

When I purchased my Scrambler the previous owner had someone install a 1998 4.0 liter out of a Cherokee with an automatic. When he installed it into the CJ-8 he installed an AX-15 behind the 4.0 liter but kept the automatic PCM. The scrambler was towed from his house because he said it would not start due to a dead battery. When I got it home I jumped the Jeep and to my suprise it started right up but had a few fuel leaks. After fixing the fuel leaks I started it up again and it would idle funny. So I hook the OBDII up to a DRB and found that I had some upstream O2 codes. After troubleshooting the problem I found that the wiring to the O2 sensors was routed incorrectly and was melted against the exhaust. After fixing the wiring I started the Scrambler up and it idled alot better. There are no codes now and the DRB shows that the O2 sensors and TPS are working. The upstream O2 sensor looks to be a little slow but works. The problem I have is right after start up when pushing on the gas it seems like no gas is getting to the engine. You can push the throttle all the way to the floor and it will buck like you are getting intermittent fuel. When this happens you can watch both O2 sensors go into the negative on their readings. Also if you leave the Jeep running long enough it will start to die like it is starving for fuel. When I have a fuel pressure guage on the fuel rail it reads 45-50 PSI. If you push in the clutch and rev the motor it will start to run fine and sometimes go away. I am wondering if the PCM could be the problem due to it is a Automatic PCM but can't think why. I also thought maybe the upstream O2 sensor was partially damaged when the wires melted. I ruled out the TPS after I did a voltage test on it (0.723 volts at closed and 4.034 when you are wide open throttle. I was think possibly the MAP sensor is bad but I am not sure. Has anyone had this problem or simular problem with their XJ and what kind of fix repaired it.

Thanks for whatever help you can give me,

Tom

Well, from what Ive read here, when you swap manuals for autos in cherokees you HAVE TO SWAP THE PCM. Search auto to manual swap.