99 Chrysler LHS 3.5L V6 with multiple engine faults

A friend asked me to look this car and I might of bit off more then I can chew. He overheated it to the point that the engine was not worth repairing. We picked up a used engine that came with the wiring harness and most of the sensors on it. We put it in, but couldn’t keep it running

I reinstalled the old map sensor and it would idle but not well. I then noticed that the battery and check engine lights were on. Thinking that not having a good charge may be causing some of the problems I tried to tackle that first. I printed out some wiring diagrams off of AutoZone’s website and checked: fuses, relays, wires, connectors, and grounds from the battery, PDC, alternator, to the connections at the PCM. All seems to be okay. I had the alternator tested and it passed. I don’t want to start buying computer related parts (something is not working, but It all worked before he overheated it.) so I thought I would take it for a drive and stop at the local parts house and put a scan tool on it.

It ran poorly and had many error codes. I also noticed that the speedometer and temperature gauges were not working. With this and all the check engine faults I decided to replace the wiring harness and all the sensors with the original parts off the damaged engine. Although it seems to idle well now it didn’t fix anything. I’m sure there is one thing here that is jumping out at me, but the wiring diagrams are incomplete. My best guess is the Power Control Module or the Body Control Module, but I can’t find any way to know for sure, and would overheating the car damage the part? I’ve been told this car has a need for a good ground. With all the grounds on this car and one is off and it does this. Well there is one sick person that came up with this car

Here are the twelve trouble codes the scan tool came up with. P0108 MAP or MAF, P0113 Intake Air Temp, P1118 Engine Coolant Temp, P0123 Throttle Position, P0406 EGR, P0443 EVAP, P0700 Transaxle control fault, P731 Gear Ratio error, P1297 MAP sensor, P1299 vacuum leak IAC , P1478 Battery temp. I did replace all the sensors and some gaskets after I got all these faults. The last test drive I still didn’t have a working instrument cluster on the right side, battery, and it still doesn’t shift out of 2nd gear. With this I didn’t drive back into town to a parts house and use there scan tool

One last thing when I installed the original wiring harness I came across a connector and can not find a place to plug it in. It’s clean so I was thinking it was connected before. It’s on a pigtail that is at the front driver’s side. After splitting off the first connection it the alternator then it goes on down to the oil pressure sensor. This single wire connector is ends about at the same distance as the last connector. It isn’t on the harness that came with the new engine and I can’t find were it was plugged into on the old engine too. It’s a blue wire with I think a green stripe, and goes back to C1 24. If this year car has two temp sensors this could be it. I know one is on top front center by the upper radiator hose. I guess I have been banging my head against the wall to long on this. I would be thankful for any insight on this