HeresToTheHeroesOhio

Hey all any help is greatly appreciated I'm a new mechanic but learn fast just need some help to get my jeep running smoothly.

I have a 96 Grand Cherokee 4x4 with a 97 4.0 motor in it, did the swap about 3 weeks ago and have been having some minor problems with it, ill start from most important to least. This Jeep had 245k on the body and new engine had 102k. It has sat in a field for 2 years but all seems fine (brake lines, ect.)

1. Stalling; Ever since the swap, it has been stalling when braking, and I'm guessing basically at times it needs to idle (Driving and not applying gas, braking, parked) My guess is either pcm screws or pcm itself. But when it starts it fires right up, we only put premium with fuel injector cleaner at every fill. Our daily driving is two footed and it doesn't run bad other than that.

2. 4wd Selec Trac Issue; The screen on the bottom by the shifter (ill call it hud) says full time, but its stuck in 4wd part time and the selector is in 2wd. If i try to engage different gears while running it makes a nasty sound or just wont budge so i quit messing with it. I found underneath that the pin that selects the different drive settings is in all angled and have to take a plate off to move it back in the right position. I just don't know where to put it back at and cant find a good diagram of it.

3. HUD Screen; It goes crazy most the time, always saying rear lamp failure but tails work fine. Coolant sensor bad, and front flashing red bar on the car part where radiator would be. Is this something I should just learn to ignore or should this little screen be fully operational?

Other maybe useful info: Check Engine light on for PCM. Not 100% but will have autozone test it again. I also did the on off self diagnostic test and it gave me codes 12, 13 and 55. No leaks, check everywhere it sits. Most major parts have been replaced and are fairly new (starter, power steering, mostly everything but sensors) Previous owner took great care and it was never abused. This Jeep hasn't seen highway since swap, would have no trouble getting to 80mph but seems rough (guessing because its in 4wd pt) Transmission also acts a little weird, shifting a little later, but i assume its the pcm.

Any input anyone has would help me a lot, I can take pics too if needed.
Thanks, Tommy