Update: So the Sunn went to jam (I'm on drums in this band, but we jam at my spot so the basser uses my rig). Everything was great. Band goes home, amp is turnned off and I want to fool around with it myself (also have to test a compressor pedal I built). Something is wrong. Noise. At first I only notice it on transients (no longer pops, but fuzzy distorted drone; not in the signal, but parallel to it). Then I switched guitars, cables, dumped the pedalboard and noticed the noise was always there, just quiet, and only spikes when there's a strong signal such as just about any note played or even fiddling with the cable/jacks. Also the amp was hot as hell and seemed a bit quieter hen normal. Could barely touch the power tranny. Quickly turned it off and went out for a smoke to give it cool down time and think it through.
Came back in and decided to swap out that iffy tube for the spare I got from Frankie. I know not ideal, but should be fine and prove whether that's the issue . Turns out that this iffy tube had cooled down completely while the others were still hot (the tranny, being a huge mass of metal, was also still quite warm but no longer hot). This made me more confident that the bad tube was to blame.
Put the alt 6550 in and everything was fine. No noise; great tone. Actually very surprised at the tone given that it's not properly biased with the new tube in; expected a little lopsidedness, like a bit of mild asymetric OD or something, but it was crystal clear and bell like. Played her quiet at first, then opened her up. That compressor pedal is working for me. Then I'm done and I shut her down. Go around back and the power tranny is still a bit warm, but cooler than before - didn't get hot again.
I hesitate to say problem solved, but I am hopefull. Since this is an intermittent problem, and that bad tube was in there at power for a whole jam, I will see how she goes at jam on Thursday when I'm on bass and if still good, will drop to the tech for a bias check while I am on vacay next week.