A little background info... 1995 honda accord with JDM H22a swap.

This is going to be a real long read but I figure that as much info as possible will help. Skip to the bottom for my questions

Ok on to the details... Ever since I swapped the engine I have had the jumpy idle up and down up and down issue. I have tried a lot of different things to fix it like replacing all vaccum lines ect. Well I got it down to where it only does it with accesories on like headlights, A/C ect.. So I figured it was the Idle Air Control Valve. Well I was able to find a H23 IACV at the junk yard so I swap it out. It still had the same issue just not as bad. So I figured the junkyard one was getting ready to go bad so I ordered a new one from hondaautomotiveparts.com but it still hasnt arrived.

Anyway after I put the junkyard IACV on I noticed the car would seem bogged down a little and every now and then it would idle real rough at stop lights at around 500 rpms just real rough and the engine would kinda shake to where I could feel it in the car. Once in a blue moon when I would come to a stop the rpm's would just drop and the car would stall out, and it would take a few seconds longer than normal to get it started back up again. That only happened maybe 3 times in 4 weeks. It didnt get bad until last saturday night, I drove the car to work and home again and it was fine, changed my clothes and went to leave again, took maybe 10 minutes started the car up drove to the stop sign at the end of my street and it died. Started it up again got to the next stop sign and it died. It died 4 times on me so I took it home and later that night put the old IACV back on since thats the onyl thing I had changed. It started up fine but once its warm it goes into the rough idle and stalls out whenever I push the clutch in after driving, it even stalls out when the car is still moving. My good buddy James(spikeddrummer) who helped me with the swap said it was an issue with the closed loop once the car is running off the sensors. I do have a CEL on for code 12 Exhaust Gas Recirculation Valve but that has been on since we did the swap but only comes on after a few minutes of driving.

Questions: what could cause the rough idle once the car is warm? I have good plugs, wires, cap and rotor. I think its more of a sensor issue. If it is the EGR valve how can I bypass it so the ecu thinks its working, I've heard of some way you can use resistors and close the circut but havent seen any instructions.

Sorry for the really long read but I figured all the info I could provide would help. If anyone needs to know anything more just ask I reply.