Well, hopefully this'll help anyone else with the same issue.. I strippped the carbs down today and rebuilt them to find petrol pretty much pouring out of them both once refitted! A second disassembly and I turned the float needles around - the small springy wire that catches onto the float lets you orientate them in one of two directions, its not obvious, but does seem to make a slight difference, so worth noting in the disassembly. I also tweaked the tabs on the floats to adjust the level of the floats slighty. With it all back together it now appears to be all ok!
For anyone else doing the same there are some really helpful videos on youtube, including plenty for the 250 ninja which has the same type of carbs.