I just read through this thread quickly but don't recall seeing this mentioned - maybe you have the hold coil and the power coil reversed at the lugs. Take a photo of your coils as installed on your CFTBL, then measure the voltages on the 3 terminals of the coil with the flipper energized and let us know what the voltage on each terminal is with respect to the terminals shown in your photo.
This almost has to be the problem - it's the only way the game could be playable with a known good fliptronics board and still have coils overheating.