Long time no post, HT!

Anyways, I just purchased a '99 EM1 with a GSR swap. Had a CEL upon buying, but figured it to be an O2 Sensor or knock sensor. Drove the car home to Phoenix from Riverside, car drives fine, VTEC engages, no big deal. Get home and check the codes and I get one for an IAT low circuit. I changed the IAT and cleared the code, code went away but then I get a code for TPS low circuit. TPS was bad and installed a TPS and calibrated it, code stays and now it throws a code every once in a while for CKP (p1337). I performed the CKP bypass, code still shows and so does the TPS. Car came with a P28 and a jumper, I bought a P2T to take emissions and the codes pop up on both ECU's (except the CKP does not on the OBD1 for obvious reasons).

I need to get this car to pass emissions before I can drive it and I'm sick of dealing with these codes. I'm pretty close to just buying a new harness as I'm convinced the harness is at fault.

 

Might have found another issue pointing back to the wire harness. Dizzy is a 9 wire (in the background, 99-00 Civic Si/96-01 Integra) but the wire harness is a 7 wire (in my hand).