The minor change in elevation of 2000 feet is not going to affect the motors performance much at all. As the motor is fuel injected I would assume the computer would change the fuel flow automatically to keep it at an optimum rate based on the altitude you are running at. Same system as an EFI snowmobile. May see a 2 to 3 hp loss max. My buddy has the exact same motor and comes out here from the coast every year to fish with us for a week and he does not have any noticeable performance loss issues.
I think the water et al you have found in the fuel system so far is a bigger factor in loss of performance. I would say after getting the water out and draining your tank if possible, then fresh gas and some Sea Foam thru the engine would not hurt it one bit. Sea Foam is available at Canadian Tire or NAPA. Afterwards, change out the spark plugs, some new fuel and should be good to go.
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