chance174

Alright so I've got a 1996 c1500 swapped with a 2001 4.3L Vortec. All of the electrical and everything that could possibly transfer to the 01 motor from the 96 did. I drove my truck about a 2 miles the other morning and I got out and left it running while I ran inside my friends house. I came back outside about 15 minutes later and it was running very poorly. I drove it and it was misfiring, backfiring, and very hesitant. Its a constant misfire and the backfire isn't exactly constant but it is very persistant. I have had the same syptoms multiple times in the past and it has always been corrected by replacing the distrubutor cap. So I replaced the distributor cap and it fixed absolutely nothing. The only codes that it is reading are multiple misfires and they're cyclinders 1 and 3 simultaneously. I believe the main difference in the problem now and the problem I've had before is that this time I think its backfiring through the intake. Ive replaced the cap, recently replaced all of the o2 sensors, checked and cleaned all the spark plugs, checked the wires, tested the ignition module, and even removed the valve cover to look and make sure that all the the rockers are moving properly and they all looked to be functioning properly to me. I took the spark plugs on the 2 misfiring cyclinders out and it felt and sounded like there was plenty of compression but I dont have anyway to accurately test it. I'm at a complete loss on this one and have no idea what it could be. Any help at all would be greatly appreciated.
Austin