Not Mustang, but the isssue came up with the bil's Escape. It had a misfire, so I scanned it. We swapped coils, and the misfire stayed on the same cylinders. He changed the computer, but had to have the dealer reflash it.
No. When swapping out a PCM you need to install ALL the software that allows the car to run and communicate with other parts such as the ABS module SJB and so forth, it's called installing "as built data". A flash tuner only has the ability to change certain parameters that have to do with the way the vehicle adjusts fuel spark maps.