Gregg, the misfire counter resets after something like 300 or 500 misfires, starts over at zero. I'm following this as it is probably different from my issue. Haven't been able to do any runs on the car with the unusual amount of snow we have gotten. After the car sitting for almost 3yrs it fired up in seconds. Idled great. After a few runs it developed a misfire all cylinders on Bank 2? Shared Plenum so I figure it can't be an intake issue but either fuel or spark. Recently I just started it up and it seemed to have migrated to only cylinder 5? I've now drained the fuel (Almost 3yrs old) and replaced with Ethanol free 93 (Euro about 99~100) Octane. Going to confirm this week if it is spark or an injector.
Cruzan, with all that said are you sure your intake was seated well? With the MAF's connected electrically and misaligned you will get a miss. You can either re-/seat them and check or just unplug the MAF's and check the misfires. Could you have gotten bad fuel, of course with our general crappy fuel additives and common 10% Ethanol fuel but like you said, I think it would have been under a load you noticed it. Anything else done recently not mentioned in your first post?