Ok.....devastated and a bit angry now. Put my South Park transformer in X-Files. New fuses. Turned machine on with playfield up and the game powered up and the music started. I then hear a crackle in the bottom of the cabinet somewhere and smoke starts coming from the transformer. Now I've fried two transformers.
I'm at a loss now....where to go with X-Files?
Thanks,
Adam.

Did you power up the machine with everything disonnected first?
You need to connect one thing at a time and check that there is a fuse there to protect the transformer.
Do you have a schematic?