Hi Skypig.

A couple of initial thoughts:
1. Check the plug caps for cracking which may effect spark performance.
2. Check your float heights. If one is out, it could be empyting the bowl quicker than it can refill it.
3. Have a squiz at the woodruff key in your flywheel. If its damage, the timing could be shifting.

Is the bike running a PGM1 or a PMG2?

Whereabouts in Aus are you? Im in Brisbane and have a lot of mc18 spares (PGM #1 and RC control boxes) which could also potentially be an issue.

Good luck with it! It will be all worth the hassle once you sort it out!