Interesting. Pretty much the only place left that flux could be is inside the transformer itself, impregnated into the material around the guts of it. That could've happened when I tried to clean the initial build with isopropyl back before the rebuild. That mixture (ChipQuik and isopropyl) may have dripped in there and dried. I'm not sure that's the case, though, as I can't see any of the chalky residue that was everywhere else. That said, everything else is either new, or very, very thoroughly scrubbed, so if it's flux, the power transformer is likely where it is.
When you say something "more concrete", what kind of behaviour are we talking? I doubt I can leave it on that long as I can't keep an eye on it consistently. I should probably be close by if something dramatic could happen.
I'll see what can be done, though.
Strangely, when I bypassed my DAC (a Topping D90) and plugged the amp directly into the headphone out on my computer (so using the soundcard), I listened to music for another 2.5hrs without any pops. Hardly definitive, but, is there anything about a DAC with an internal switching supply that might cause issues like that popping? Doubtful I know, but I'm keen to rule it out.
Also hoping to rule out the thing with the sanding the sides of the power transformer - could sanding the coating off the sides and then blasting it with paint have caused some issues?
One other thing - it seems to be more common with more sensitive headphones than with speakers or high impedance headphones. That may be some other factor at play, but if it provides any clues...
Thanks for all your help.