When I said "before we jump to conclusions" I was really hoping, being an 09 bike, it wasn't the gearbox problem rearing its ugly head again.

Sorry that it appears it is, and I hope you get it sorted quickly and cheaply.

FYI - XTR/X and MT-03 engines will all work as a donor. This does widen your options slightly. Also bear in mind MT-03 models generally seem to cover considerably less miles/Kms than XTs.

Very bad news. So sorry to read about your gearbox issue.

Is it time Yamaha recognised this as an issue?

Quick update, after reading several posts with photos of the internal damage I decided to fit a new engine. Got an MT-03 with 8,000miles all fitted and running great.
Got a winter project now stripping the old engine to see what damage was done.

Well done, mate. I sure hope you have a great run out of the new motor.