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Purchased a 1996 Civic EX about a week ago and knew it had an exhaust rattle when I bought it. Was clean, 140k miles on the dash and no check engine light on. I drove it and all seemed well until I went to fix the exhaust. I don't know much about cars, much more motorcycle oriented and the muffler guy, who had some Honda knowledge, informs me that it's not the original motor.

I'm supposed to have a D16Y8 but I currently have a D16Z6. Well this is illegal so I may never pass state inspection with it but I'm going to try. Over the past few days I've read a lot of the swap posts and that but my problem seems to be specific. Here is what I have:

Motor: D16Z6
ECU: P2E (for a 96-2000 DX)
Harness: Looks like the DX harness as well, 2 O2 sensors, one on the manifold and one near the firewall. Not as far down as an EX.
I am throwing 4 codes, 3 are related to not having a catalytic converter and then P1337 which is the CKF sensor. Aside from that the car works fine, getting poor mileage but I expect that with no cat and an exhaust leak.

So my question is, should I revert it back to OBD2A, put the correct ECU in with the correct wiring harness or should I throw a P28 ECU in it as I'm assuming it already has the jumper in it because it is currently running on OBD2. A little overwhelmed at the moment so I may have things completely mixed up but any help is appreciated. It seems if all the work for the OBD2 system is working I should just throw in a P28 and I should be good if the other work has been done? Other work being the injectors, alternator and dizzy.