Ok, just had a good long while to test a bunch of different things. The problem is back with a vengeance. Turned the amp on for about 45 min playing through it at band volumes straight in. Bass > Cable > Amp. Everything seemed to be working fine. Tapped on all of the tubes (preamp, driver, and power tubes) and got no strange sounds.
Then, plugged in my pedalboard. Tuner > Compressor > Fuzz > Preamp. The crazy broken up sound immediately started. I double check to make sure it wasn't any of my pedals causing the issue, so I checked all the patch cables and everything seemed fine so I plugged directly back into the amp again and the sound was still there now, like the increased volume from the pedalboard had shaken something up causing this issue to happen.
I just tried wiggling the input jack on the 0db and 15db inputs and it's crackling loudly when I do that. Thinking those solder joints might be bad. I'm going to reflow the solder there and check it again in a few.