Alright so just in case anyone is having the same issues, since fixing the trans sub-harness wiring the neutral switch code went away and my slow response oxygen sensor (O2 sensor) was still popping up. Took a look at the plugs and my cyl 1 plus porcelain was cracked and I was using the wrong heat range for the boost I was running!
I switched from a SILFR6A plug to a LFR7Aix plug and gapped it down to .025" and since then the car hasn't thrown any codes since.