Honestly, these traces are making me feel like I’ve been taking crazy pills. If I had any compatible ROMs at hand I’d be tempted to make a NOP ROM for my PET and see if I could get a decent trace off it, because this still feels like something is wrong with the triggering here. Putting the trigger on the highest address line *should* give you a reliable timebase; that is a reference that will complete a full cycle once per iteration, and regardless of whether you triggered on the high or low slope the instructions following that transition will consistently be 2-cycle NOPs. (Over 4000 of them after each transition.)
I chucked out the idea earlier of building a single-stepper, that’s sounding less dumb to me.