At least two observers think the culprit is not transmission and despite your list of improvements something got overlooked.
To review the symptoms and improvements so far
Sudden onset of vibration following abrupt over- reved forward gear engagement. Polished drive gear at the clutch (cone) engagement surface presumably the forward gear. New mounts, new shaft, cutless, motor alignment, propeller balanced.
This group of facts probably rules out drive gear slippage because the polishing took a good long time and there are no other obvious transmission parts implicated. While the gear surface coincidentally needs a 600 grit scuffing that condition is not responsible for sudden onset of vibration. The condition is also not a failure to re-align on water, nor mischosen or misapplied motor mounts because these cannot explain a sudden onset either. A propeller balancing session - which suggests a fixed prop. But why balance the prop to start with? And how much balancing work was required? However, the prop is not fixed it is a Martec.
For sure diagnosis from afar is a tough job. But so far - from a differential standpoint - my money is on damaged propeller blade deployment mechanism.
Charles