TT600r doesn't like the rain!

[wonky]

My 1999 TT600r Belgarda doesn't seem to like heavy rain.
Basically, in a heavy storm when cruising at above 50mph the bike starts to cough and splutter(as if it has hit the reserve fuel level) and then stops firing. Cranking the throttle open doesn't help, but it has started again a couple of times if i just leave it coasting along
After i stop, I leave it for a couple of minutes and then it kicks up fine.
It happened once in England in a massive downpour on the M1 at about 80 in the fast lane, but i figured i must have gone through a massive puddle and flooded it.
I had the problem again trail riding in Wales.
Now i'm in Vietnam in the rains and its getting to be a right pain.....
There doesn't seem to be lots of water in the airbox.
The rubber cover on the spark plug doesn't fit properly over it. Could this be causing it?
Water in electrics?
Other than this the engine runs good, although i've been having a problem with the throttle sticking open which isn't cable related(i changed it, oiled it and set it right). I oiled the return spring but haven't checked the second carb lever thingy, the problem seems to be on larger throttle openings so maybe its that. Could this also be some sort of intake gremlin?
After fitting an Arrow Dakar(?) can I had a really bad dyno reading a while ago so maybe ive got general carb bother. Putting a big 160 jet in seemed to help, but ive not had it dynoed since.
Any ideas?