Civ2000

I wanted to brainstorm with some honda ppl, so here is some history before we start.So i got this 2000 civ ek coupe. the guy before me swapped the d16 out for a b16 engine, put a ktunned ecu and obvs. was tuned. although it was running great when i first got it, i never felt the vtech kick in. after doing some research i figured id clean it up and bring back "stock" meaning acquiring a stock b16 ECU and possibly a stock b16 wiring harness.So i procided by changing the ECU first (later was told that it was the wrong decisons from someone i know personnaly). the car wouldnt start, so i did some more research, and found that the engine was missing a ground so we added it and cleaned up the terminal wires aswell and never had a problem with it starting since. but i need to clear this CEL and have been told to put the odl ECU back in but i tried that and the CEL was still there. the codes that are coming up are P1259/ P0135 / P1337 / P0141. I need some advice about this stuff.
Ive talked to the one who did the swap and he told me that i cant change the wiring harness since its all one piece and pretty much called me an idiot. So i am stuck and need some help please.