It actually turned out to a carburetion issue... float bowl overflow tubes (after taking the carbs off and stripping the internals a bunch of times!)
I had heard something about this before, someone had said that their carbs had been sucking rain water up through the overflow tubes and into the float bowl, the problem is cured by cutting the ends of the tubes at an angle to stop droplets forming over the hole... But, mine were already cut like that, plus I had checked on at least two occasions whether there was any water in the float bowls, and there wasn't, so I had decided that it wasn't the problem.
That was until, after a stroke of genius, well really just desperation and 'try anything and everything' logic, for some reason I pulled one of the overflow tubes off and blocked the overflow outlet with my finger, and hey presto that cylinder started to cut out after a few seconds. Seems as if blocking this creates a vacuum that either cuts off the fuel to that bowl, or the exact opposite causing it to flood.
The problem didn't always crop up when it was raining which led me to believe it wasn't caused by water, in hindsight it was either wet road conditions or the day after rain etc. I guess there was water residue/droplets in the tubes that only created a problem when there was significant enough draw/vacuum on the float bowl i.e. high revs etc. Which would explain why I could leave it idling for 15+mins no problem, but after riding it for a bit it would start dying on me. Also if it drew the droplet all the way into the float bowl the problem would clear up I guess, which would explain some of the intermittency.
Bit of searching, I came up with this:
http://forums.sohc4.net/index.php?topic=107640.5Looks like they are the only vent from the float bowls to atmospheric pressure. Running them without the tubes at the mo with no problems, but a clean and reroute should fix it. They're the PD carbs if anyone is having similar issues.