I recently got a performance PCM reflash done by a recommended business and just recently after two weeks waiting, got the new PCM.
Opened the box and found that one of the harness bolt holes had a bolt snapped off inside, and it wasn't coming out. I had to drill it out in order to get the harness to fit snugly.

Started the car, and almost immediately, it started running rougher. I had it tuned for premium and no cat. I drove down to the exhaust shop to get the cat removed. On the way, it seemed to be getting to much fuel under throttle, and then the SES light started blinking rapidly.Parked the car and walked inside. Came back and the car wouldn't start. One of the mechanics scanned it and got Codes 203, 303, 403, and 449. Mostly pointing at the #3 cylinder as causing issues. They lent me a car so I could go home and get the old PCM. Quick install, and the car fired up and ran perfectly fine, like it had before.

Before I call this company in the morning, I want any ideas for any reasons that the newer PCM might have done this? I just want to make sure I am covered and can work this out. This is the last major power addon I am doing for the car, so I want it to work out.

Oh, and I had the shop leave the CAT on for now. Figured there was no point removing it if the PCM wasn't tuned right.