So with the magnets disconnected the fuse still glows hot.
Maybe something driving that circuit is feeding too much juice down the line.
Send Beaky a PM and grab his phone number. He is the BEST pinball tech in Australia and understands every part of a pinball machine extremely well. I am sure Andy would spend half an hour with you on the phone and walk you through exactly what and how he would trouble shoot your problem.
I think a multi meter and checking what is coming out of your boards would be where I would start to determine if the values are correct or not. Once that is established and checked, you can then work down the line on each component.
Phoning Beaky could save you hundreds. Ask him in your PM to look up Thatre of Magic schematics before he rings you so u both have them on hand at the same time.
