Motorcycle Repair: Rough running fuel injected FLHT, water in the fuel, wet weather

Question
Took my bike for a spin after 24 days of wet weather.  I keep her plugged to a trrickle charger, fuel full up, and coverd on carpet.  Did my pre-ride checks, warmed her up to op temp and scooted out.  Ran about two milesand one-half miles to the freeway.  Moved onto the freeway in quick order shifting throught the gears around 3 grand.  Started to spit and sputter and loosing power.   Pulled onto the shoulder, cleaned the plugs, rear one was abit foul but dry?  Nursed he back home running rough.  I have added some fuel stablizer, thinking I may have some water in the fuel mix.  Any suggestions to get her running smooth again..

Answer
I would start by replacing the fuel in the tank and see how it runs. You also might have a plugged injector. Try some injector cleaner and see if that doesnt help. If these fail then you are going to have to take it in and have a dealer do a dianostic on it.
Good luck and happy riding
Mike