Trouble code CPS issue

Vehicle: 1996 XJ Country 4x4 w/4.0L, AW4 w/190k. I replaced my CPS recently. Along with that I also replaced the distributor, rotor and the sync sensor in the distributor. I was getting trouble codes 11 and 54. Everything was fine. It was running like a top. I decided to de-grease some of the engine. Bad move? It started running rough but cleared up. Drove around the block a few times to check and everything seemed fine then.....it started running rough then would not start at all. I got it back to the house with a tow from a friend and after a while I could start it and it would idle just fine. Try to race the motor and then it would stumble a bit. Cleared the trouble codes and now all I get is a 12 saying I've disconnected my battery within the last 50 starts. I suspect a possible fuel filter going bad? I've never replaced it and I bought it with 125k on it several years ago. Am, I going down the right path?

Nothing wrong with preventative maintenance in the form of filters, but I can tell you that the Throttle Position Sensor does not like getting wet. Excessive moisture on/around/in the TPS can lead to running issues, AW-4 shifting issues, and TPS failure. If you have OBD-II you should download the four digit OBD-II trouble codes. The OBD-II codes are much more specific than generic OBD-I codes as to the problem, and where to begin trouble shooting.

Did you clean the water out of the distributor cap?

I would take the distributor cap off and make sure everything is dry.

Ok, the Jeep had been sitting all day yesterday with the battery disconnected. This morning, using the ignition key method, I checked the trouble codes and all I got was 12 which indicates the battery had been disconnected within the last 50 key cycles. I do not have an OBD II meter. I did blow out the TPS as well as the CPS plugs. It does start and run smoothly in idle and when I race the motor.

On an unrelated issue, my transmission will not shift into second gear. It shifts straight from first to third. I have purchased a solenoid replacement set and will install those. I believe the problem it's having is caused by the one solenoid, 1-2 but I will replace all three since I'm under the XJ. I have a new tranny filter as well.

Thanks all.

I suggest you download the OBD-II Check Engine Light trouble codes and gain some insight into the cause of the symptoms. As I said preiously, a wet TPS will likely cause AW-4 shifting issues.