Ok so I disconnected the alternator, and there was no change in the engine.
I plugged the two black wires together and I got these codes.
32 Oxygen Sensor or Circuit
35 Purge Control Solenoid or Circuit
41 Air/Fuel Adaptive Control
22 Knock Sensor or Circuit
24 Air Control Valve or Circuit
What do you guys think?
Considering I allready had a little issue with the wireing harness could all of his these things be running on one plug or something? Also the engine sat for about a year before the swap... could all of these sensors be bad?
I could be misreading but I think you said you are missing 1 plug on the intake manifold harness that was the smaller of the 3. That one usually has mostly sensor grounds in it if I am remembering correctly. It would certainly explain all of the codes, in essence "ghost" codes as the sensitivity is too high (sorta).
You really need an entire engine harness most likely the battery corrosion got into those connectors. Lots of patience, de-pinning the main harness side, cleaning with a brush and dielectric grease coating after, might also work.