So I have been slow and all that but I have gotten around to checking the input voltages for the PWM chip and they were pretty good. So I swapped the two main fast switching transistors and saw a voltage much closer to normal.
I swapped in ones from a unit that already was suspect for having bad transistors, so before I proceed I want to replace them with a modern equivalent if possible. They are marked C3042, and I'm guessing that is equal to a Sanyo 2SC3042. I found one I think might work as a replacement - a Fairchild KSC5338D, what do you think?
The current problem I don't know if there's still something wrong with the transistors, but the voltage varies a bit when it's turned on, depending on how long its been off. Perhaps the issue will go away when it's under load. Also, -12v is not working, so I guess I'll be hitting the schematics again for that. I don't think I really understand what negative voltage is yet.