Done! Third time's the charm. Everything fits and no stroke interference. I gave it a brief run-up tonight and it hit 1296 RPM at 100 watts using the electric heater. For this I was running with the thicker flange displacer cylinder.
The engine is much quieter and smoother. It starts running with the new lighter flywheel after 4 minutes of warmup (the electric heater at 100 watts is somewhat slower than Sterno was, I believe) and starts at about 700 rpm, gradually increasing as the furnace heats up.
There seem to be stages of steady rpm, then increases to higher levels, where again it stays relatively consistent for a time before increasing. Maybe its some set of resonance levels. There's a fair amount of vibration (for a small engine) and I notice that if I place my hand on it to steady, I can sometimes get an increase in RPM.
I think balancing the crankshaft might help top speed, but not sure how to do that with an inline twin with a 90 degree phase difference.
Anyway, here it is with new flywheel, new power piston conrod (ball bearing big end), and new crank arm: