I'm watching this thread, will be interested to know what the problem was. Have rebuilt a couple of 2 stroke outboard motors but I'm no 2 stroke expert. One of the 2 strokes I rebuilt was a 1982 70hp 3 cylinder Mercury (cylinder head is part of block casting and can't be removed), put new pistons in that (pita putting them in from the crank side), then it ran OK for a while but suddenly had the same symptoms as your engine that I never got to the bottom of.
Now after reading others posts on this thread I think maybe the problem with my Mercury 70 was a reed valve, crankcase leak or top seal. I don't know how pulling the head might help reveal the problem but if 2 stroke experts said that was a good idea that's what I'd be doing... as long as they were willing to re-engage and talk me through diagnosis after pulling the head, otherwise after checking the inlet and exhaust ports seemed to look the same on both cylinders I wouldn't know what other checks I could do that could tell me something the compression test hadn't already provided critical information about. It would be nice to know the reason for pulling the head before doing it but if experts didn't want to explain each step in their thought process I'd be happy to go along with what they said anyway, doesn't seem a lot of work to pull the head off the 2stroke.