2000 jimmy rough idle

hi I have a 2000 gmc jimmy with a rough idle here is the story I bought this truck with a blown intake gasket and a misfire. I replaced the intake gasket during disassembly I noticed that the #4 spark plug wire had been rubbing on the ground strap and looked like it had been arcing so I did a complete tune up plugs,wires,cap,rotor. I got it all back together started it up and noticed it has a rough idle but if you give it gas it clears up and runs grate it is setting code P0303 so I swapped plugs no change swapped wires no change. I know these engines have problems with the poppet nozzles getting clogged so I replaced the injector unit with the upgrade MFI unit but did not fix. When I was replacing the injector unit I noticed a lot of carbon so I checked the EGR valve it was not stuck open and the pentle moved up and down without sticking. I also looked at the MAF sensor it did not look dirty also checked PCV valve it looked like it had been replaced I shook it and it did not stick. I checked fuel pressure key on engine off 60 psi with the engine running it has about 55 psi that may be a little low but would that cause a misfire on cyc 3 only? I don't think so but I guess any thing is possible. I have also compared compression with the #1 cyc they are both 120 psi after cranking for 3 seconds. thanks for reading if any one has any thoughts I am open to suggestions.

Did you pull the plug back out and check for a defect? You can try using a spark meter, too see how strong of a spark you have at the plug wire. Did you verify your timing after installing the intake?