Advice Requested - Traxter Water & Starting Issues

Also posted this under the General Can Am/BRP forum...

I have a recently purchased 2001 Traxter 500 (Elec. Thumb Shift) w/600 miles. Up until this weekend it has run fine, but only around the neighborhood...nothing too crazy. I took it out this weekend with my daughters and got out, off road. Crossed a creek (12-18" deep), rode around on the "mountain" trails for about 30 mins w/ no issues. Came down the mountain and then decided to go back up. On the way back up, after bouncing over a small downed tree, the machine lost power and died. Tried to start it several times w/ no luck. Found a little clear water in the air box. Let it sit for a few minutes and then she started back up and idled, no choke, for several minutes then died again. Towed it back in and let it sit overnight.

The next morning, drained the carb, removed and checked plugs (got fire), checked oil (found it milky w/milkshake on bottom of oil cap), found small amount of clear water coming from crankcase/valve cover vent through PCV valve (PCV still woks) & coolant in reservoir is full and very clean. Changed the oil (10w40), removed and cleaned the carb and blew out jets and she started back up easily. I drove it around for about 30-45 minutes and noticed that at higher RPMs in each gear the engine would hesitate or stutter a bit unless I gave it more throttle or shifted. Returned back to camp and again, found a little more water in the air box and a slight bit of water droplets on oil cap. Started again (no problem) to trailer it and then took it along bumpy road to another area. Later tried to start it again, and it would almost start and backfire several times, but no luck. Now it won't start at all, just turns over.

From the oil standpoint, clearly the unit has taken on water to some degree before I owned it, but I'm also puzzled over the clear water in the air box. Not sure if I've got two different issues or if these are related. I was told when I bought it the oil had just been changed and I believe it had because the oil was clear, but I now suspect the oil had been changed in response to taking on water, but had yet to become milky.

My gut says the not starting issue is still something with the carb, but I'm curious what others with more experience on these machines my think.