Hey all, so I broke the injector on cylinder 4 trying to remove it in the recommended way using two screwdrivers to pry up on the plastic tabs, as I wanted see if it was leaking or stuck open. Unfortunately, the screwdrivers went clean through the top of the tabs and I had to resort to vice gripping it out. It got pretty banged up from the vice grips, so I ordered a new injector and new o rings, threw it in, and this actually solved my problem.
Essentially, the car ran fine with the auto ECU, and between when I turned the car off and installed the manual ECU the next day, that injector either died or stuck open. I believe it was stuck open due to the raw gas smell from the car when it ran on three cylinders.
Moral of the story, just because you recently changed something, doesn't mean your new issue is from that! Thanks for the suggestions everybody!
