My best guess is that the amp is running hot because you messed with the bias adjustment. As a general rule, you shouldn't go twiddling pots in gear unless you know what they are for and how to adjust them. You could do serious damage. Here's the manual with bias procedure on the last page.
Start by adjusting it according to procedure and then let us know what works and what doesn't. I suspect the original problem was likely switching jacks or a connection issue.
P.S. Welcome to the place!