w0lvez

It's running very very very rich. His Injector's flow rate is more than 4x compared to the stock injector.

ScrewThat

Man I'd love to see what his afr is. Lol

Allaround4x4

According to everyone, way too much. But I returned it to stock and all of the problems still exist. Even the transmission

w0lvez

The problem still exist probably because the Clogged Catalytic Converter and Fouled Spark Plugs. Vacuum test your Engine.

ScrewThat

Don't put those injectors back in until you have the supercharger on. Clean the stock injectors just to rule any issues with them out. Then I'd change at least the plugs with motorcraft plugs. Coils probably wouldn't hurt either but if you don't want to spend money on all 8, you could go through and replace any that are faulty. Take your boost a pump off because you don't need the extra pressure with stock injectors. Hell I'd even put a stock fuel pump back in it. Then I'd check the catalytic converters. There's a decent chance that they overheated due to running rich for however long those 95 pound injectors were in there with those pumps and melted the substrate which would cause flow blockage. There's no real simple way to check the converters so I'd take this opportunity to ditch the 4 factory cats and install two good high flow cats. Might could even do headers if you're interested in those.

Basically get the engine running well first. There's a chance that it seems like the trans is acting up but In actuality it could just be a severe lack of power causing it to feel funny when it does shift. If it doesn't go away then I'd diagnose the trans. It would be two separate issues at that point.