Civic VX CEL/rough idle

[FRUGALnotCHEAP]

Hello everyone,

I am new to this forum but I have always had an interest in Eco modding. I am attempting to mod a Honda Civic hatchback. It started life as a 95 Honda Civic DX, but then I bought a wrecked 92 Civic VX and swapped the engine, transmission, wiring harness, computer, lightweight rims, and all of the extra emissions stuff that came with the VX. It now starts and runs, but I am having a problem with a rough idle, and a check engine light. I tried to pull the codes from the ECU using the Honda paper clip trick and the flashing check engine light, but I was unsuccessful... just a solid light and no blinking. I've done a few things to try to address this issue but nothing has worked. I changed the plugs, wires, cap and rotor. I thought I could hear some kind of intake whistle, so I changed the intake manifold gasket (but I was not really able to successfully remove all traces of the old gasket, nor was I able to get a torque wrench on the nuts so I don't know if they're even evenly torqued, so maybe that made the problem worse?) I also replaced the vacuum lines in case there was a leaking one. So far nothing seems to help... I need to get this car running Tip-Top so I can start doing the mods I want to do. Any ideas?