Did you try the preamp tubes? Look at the back of the amp while it misbehaves. Any of the tubes sparking or flashing? Don't forget the rectifier tube too.
Set up a loop or delay & set it up so the amp misbehaves. Do any of the controls affect it? Which ones? Ball up your fist while it misbehaves & give it a firm whack on the top. Does this affect the noise in any way? (This is called The Enzo Whack in these parts, and is kinda patented. Or you can use a rubber mallet. Don't hurt yourself & don't break the amp of course.)
Also, R.G. Keen's Tube Amp Debug page is a great resource to start out. Geofex.com, look in top left corner & find "tube amp debug page." Follow links accordingly.