Well, I'm still having misfires after the harness was replaced. It was driving fine in the city, but about an hour into driving on the freeway and it threw a P0430 catalytic converter efficiency code. I was heading home for the holidays so I wasn't able to deal with it until I got home a few days later, where it also ended up throwing a P0308 (cylinder 8 misfire) code.
I wanted to do some preventative maintenance anyway, so I replaced all the ignition coils and spark plugs (except the 8 exhaust ones) with brand new NGK ones and I gapped the spark plugs to 0.030 as recommended by JDM due to the supercharger.
After that, it ran great on city streets, but under heavy acceleration on the freeway it threw codes P0308 and P0306, the engine sputtered, vibrated fairly violently, lost power, and the CEL was blinking. As soon as I exited the freeway and got back on city streets, it ran fine and the blinking CEL went away.
I found out my battery was bad, so I replaced it with a good battery and tried again. The exact same thing happened, except it only threw a P0308 code and NOT a P0306 code and there was the sound of something clanking. But again, it ran just fine on city streets afterward.
I hit the catalytic converter with a mallet and didn't hear anything rattling around in there, but other than replacing the final 8 spark plugs, does anyone have any suggestions on what it could be?
I also plan to take off the valve cover to see if the valve springs are in good shape.
