is the evidence of heat black or white looking, or, more brownish? black/whitish deposits i would think would be indicators of crazy-hot arc temps, whereas brown toasty looking colors would be more of a sub-1000F "baking" type heat.
as far as spacing and holes, virtually all of the output tube heat is created above the PCB surface, and heat rises, so...heat produced by the output tubes should not be much of a factor, IMO, assuming the amp is used as designed, ie in the upright "attitude"...
the ceramic sockets shouldn't conduct much heat back down into the PCB either.
maybe some of those PCB traces are arcing over to something else? those nuts look awfully close to the tube base contacts, but i assume thats a tried and true design.
maybe you should operate the amp upsidedown and apart, so you can look at it when the crackling sound is actually occurring?
just my 2 zimbawean cents
I just noticed that the PCB around my output tube sockets looks like it's been getting hot. The board replacements did not have the socket holes with the notches on the sides for extra airflow and I didn't know how to do it without wrecking them. So when I put my ceramic sockets in they just barley fit so after they warm up could it get the PCB hot enough to cause my intermittent problems? Here is a older pic showing the output sockets I'm talking about but this is when it was new so you wont see any heat effects.