Well I guess we should never underestimate the ability of a little bit of water to mess up an entire fuel system! I drained all the fuel from the tank, filters and fuel rail and then had a look at the final product in a clear bottle and sure enough, there was about 2 oz of water in it.
Hunted down the place that sells fine Australian fuel (Versus the stuff they buy from Indonesia) and began a system of filling a large, see through gas can then allowing it to settle for a minute then pouring the top into the bike and leaving a litre or so behind and hopefully any water or sludge with it.
The bike runs like it should now and the overheating issue is gone as well!

Of course the max speed here is about 30kmph because of road conditions so I'm in second gear all the time but it feels nice to be running right!