Gt in October 2013 spun a rod bearing on Cyl #5. Didn't replace the bottom end until just a week ago.
Everything went in fine. Replaced with PowerSeal Crank Main(25mm) Rod(50mm)
After putting it all back together. It ran rough. Throwing all o2 codes it could, blowing smoke out and misfiring with cyl #2 40psi on compression. Did some investigating and found out where the Lifter on cyl #2 on the intake side jumped off. Causing the smoke and bad compression. The chain on bank 1 side had jumped time due to a bad timing tensioner. Replaced it and put back into time. No smoke but still a bad skip with o2 codes. Found out the EGR valve wasn't bolted correctly. Which fixed all the o2 codes.
Now it's a misfire on cyl #1 replaced plug and coil pack and still a skip ins the motor. I'm being told it could be in my tune.
Would a tune cause my computer to throw a misfire code?
Or a bad Alternator? My alternator does fluctuate in power. You can see it in my headlights.
Or something worse? I'm just out of ideas. It is running very rich.