Ok so here is what I did today....
Frist Drained the transmission oil... It was not milky at all... Perhaps very very very slightly grey but not mikly for sure... I would say little to no water got in there.
I then proceeded to remove the air filter, I noticed some sandy shit got in the carbs so I took them off, took the bowls off and cleaned the heck out of them and put them back together, took the reeds out as well (I have a set of Vforce2 reeds I bought on ebay coming in the next day or two), I then looked at the pistons as best you can through the reed ports and all looks good...
I got the idea however that there might be some water in the bottom end of the engine so I basically stood the bike up on end and tilted it back and sure enough a bunch of water poured out.... I got as much of it as I could so I think it will be ok.
I will put everything back together after I get my reeds in the next day or so and hopfully all is well.
Anything I did sound odd or do you have any other suggestions of things I should do?
Thanks!
C