Thanks Gnasher, the link to ncjetski looks promising 

I'm now back on the road.
I completely drained the tank, filter and pump and then finally the float bowls; took the filler cap apart to get rid of the rust and tidy it up, filled it up with some fresh petrol and away it went. One hiccup within 30 seconds but afterwards was running cleanly for 10 miles.

Does anyone want to buy 12.5l of what I assume is water contaminated petrol??!@

Thank you so much for this very old thread. I had the exact same problem, with the exact same solution 

After testing the pump and taking the carbs apart, I found this thread.
I simply drained the tank and fill a few litres of new petrol in it. There was quite a lot of hickups still, since I didn't drain the fuel pipe, filter or float chambers, but it finally swallowed all the bad petrol and got back to normal operation.

Learning: Don't leave the bike in heavy rain for a long period with only a few litres in the tank