Hi Ian,
Sorry to hear about your latest tribulations in the quest for more power!
I've been giving this latest engine problem some thought and have re-read all posts and carefully perused all the photos. Old guys like me have to peruse things....takes a while to focus...
Anyway, I find the location of the scuff/pick-up marks on the new piston to be rather suspicious. These marks are very close to where the cylinder studs are situated... You also mentioned that the barrels seemed to be a bit tight on the studs. To me it looks like the studs are pushing against the side of the stud holes nearest to the cylinder bore. Usually there is clearance around the studs and the barrel spigot is accurately located on the crankcase or stepped studs or dowels are used at the lower mating face of the barrel.
Many years ago, I dabbled a bit with overboring air-cooled motorcycle cylinders. (beyond what was commonplace and defiantly (I was young then!) against the advice of experts!).
Some strange things could and did happen. The cylinder needed to be able to expand without constraint. The cylinder didn't necessarily expand equally in all directions, i.e. the cylinder bore might not be circular when hot (or very hot!). Trimming cylinder fins (e.g.to make a different cylinder fit an engine)
could and did result in distortion of the bore. Cylinder bores don't expand equally from top to bottom. But hey! pistons are not truly circular nor the same diameter from top to bottom. If the cylinder wall is reduced too much in thickness, it can distort unpredictably in service. Cylinders get hot when being bored, so immediate measurements can be unreliable.
Enough rambling, I hear you say!
If this was my engine:-
I would open out the stud holes in the barrels from the top down maybe 3/4 way.
Investigate (if possible) if these pistons have expansion-control (Invar?) metal struts built in. Iirc, original Fiat pistons did, after-market pistons might not have. If not I would increase piston to bore clearance. My rule-of-thumb on a slightly modified engine is that the piston, without rings fitted, should easily drop under it's own weight when placed into the cylinder but not rattle.
However, if piston to bore clearance was insufficient I'd expect you would have experienced trouble much sooner and the damage would be similar to what you showed in your post
#1 i.e. centrally on the thrust face of the piston skirt below the rings.
I'd measure the pistons to check they haven't distorted (unlikely given how small the tear marks are), clean off the scuff marks, check the rings aren't pinched in their grooves or otherwise damaged. In an ideal (i.e. money-no-object!!) world, new rings would, of course, be fitted but I don't live in such a world! I wouldn't even bother removing the rings to check them, too much chance of breaking them.. Just check they rotate freely and side clearance in correct, if you have a thin-enough feeler gauge. (You could use a strip of aluminium foil).
As regards one cylinder seeming to have been running a bit weaker than the other?
Maybe it was because one cylinder was running hotter due to increased friction. Are both spark plugs the same heat range, same brand, same tightness (approximately, a loose plug can alter it's heat range!). Any mods to the air cooling system, missing baffles? restricted air intake? air outlet?. Any restriction in one exhaust pipe?
As another poster has suggested, check the ignition timing is correct on both cylinders.
Imho, you might have gone a little high with your compression ratio.
Just remember that this engine ran well when first assembled, I'm sure you'll get it back to running well before long with minimal expense.
P.S. There's a reason I keep a roll of emery tape, needle files and a tin of Brasso beside my workbench.... (hint! hint!).
Al.