I know it may sound crazy, but check your air filter. Same thing happened to another member in the 4.0 section. Ford techs told him his air filter had come loose, causing the engine computer to detect a problem and the computer shut down the car’s engine.

 

I just checked the connections on everything, it all seemed to fit pretty snug... But I went ahead and re-tightened everything just to make sure. I flashed it back to the 87 tune, I'm not sure if the tune I had installed was 93 or 91 since 93 is pretty scarce around here. If it was 93 could that be the problem?