Might be worthile having someone else give it a good looking over. I had a similar situation after I installed cam and other upgraded parts and was having trouble with the engine running right (timing was not a problem). Went over everything a couple of times, no problems found. Then a buddy came by and casually remarked that I was missing a bolt on the EGR valve. Sure enough, it must have loosened up and backed out with the vibration of the rough idle I had. I must have looked at it half a dozen times and each time said "No, can't be the EGR valve, it was working before I tore the engine apart". But just like the EFI fuse, check everything (AFM, TPS, cold start injector, cold-start switch, ignitor, etc.) and take the position of proving that a given part is good with the tests.