Precision Power PC650

I do think there are two different problems, yes.

Yes, and if we can't resolve all of them, it's the last one that is the loudest, that I would like to solve at least.

No, this amp does not have adjustable bias or dc offset pots so no bias headers either.

What is the purpose of CR29 and CR3? They are the diodes physically located near each regulator. They are connected between the main rails and the outputs of the regulators. They allow secondary voltage (minus the .6V drop) to be on the rails before I switch main power on. Seems like if those were to ever short it would allow main rail voltage to be on the secondary supply.
 
I just want to add a few of my own notes that may or may not be helpful to you, Perry, or future searches. Then i'm backing out.

1) I see the small signal caps that sit under the daughter board are not fully seated in your photo. On the PC450 model the tolerances between the daughter board and the main board are so tight that these MUST be fully seated or the cap tops make contact with the bottom of the daughter board. I don't know if this tolerance issue is present on this model, but with the daughter board installed you need to ensure this is not happening. They used a plastic insulator under the daughter board on the 450 to assist in preventing this.

2) Likewise all of those to92's you see folded over to accommodate the daughter board need to be checked to make sure none of the legs are touching the exposed legs under them. It's difficult to tell in your photo because it lacks dimension. But it's always good practice to make sure.

3) Occams razor. If the only difference between now and 8 years ago was 'sitting on a shelf' then you must consider the most perishable components. Or the problem was present at the time and you simply did not notice it.