I must admit the idea of a piston skirt hitting the crank is not one I would have thought of. But I think it's unlikely. Pistons don't expand uniformley -that's why they're made barrel-shaped so they're round when hot. The top of the piston will expand more than the skirt - that's upwards. The conrod will lengthen with heat too, counteracting any growth downwards of the skirt (because the alloy rod expands more with heat than the cast iron cylinder).
But I know how you feel, GB. Despite meticulous attention whilst rebuilding my GF, I had a pile of grief with it. Lots of odd things that never happened before with other bikes, which is why this forum is so useful.
There have been a number of suggestions as to what may be causing your noise, and clearly you're not going to be relaxed until you've found the culprit. If it were my bike, I'd run a piece of straight-grained wood over it as a stethoscope. Hopefully that will pinpoint the area, though it's not guaranteed. Engines can be funny things - I recall one car engine (can't remember exactly which one now) where a noise obviously from the flywheel area was actually coming from the front. Or a slight knocking noise from a 6cyl marine diesel engine which turned out to be the crank broken in two places.
Anyway, assuming the noise is not from the chaincase, it's tank off and check tappets. If OK, start disassembly, taking careful note for witness marks of anything untoward. You shouldn't have to go any further than lifting the barrels (leaving pistons inside) which would enable you to check camshaft and bottom of piston skirt. There's a minefield of other stuff that could be a cause of noise, for example new pistons in old bores will cause the top ring to clatter or even break unless the bores are honed first, or the profile of new cam followers not being exactly right for the cam. The list is almost endless. If it's any consolation, my newly-rebuilt GF makes quite a few noises I didn't expect, but I'm not too concerned because after 50 plus years of rebuilding most types of engine I'm fairly confident I can tell the difference between something irritating and something that needs investigation before it gets serious.