(Sorry about the long story - may help you diagnose the problem and solution.)
Last Sunday left on a 330 mile trip to fish with a friend, bike running great. Stopped for gas and after filling up, noticed there was a tanker truck parked on the premises. (Yes, I have heard you should go to the next station when you see that, and no, I wasn't paying attention.) Go over a hundred miles, bike still running perfectly, and am within 50 miles of my destination when the bike suddenly won't accelerate.
There is maybe a five minute period where I can maintain 60 mph but without the usual acceleration when I roll on the throttle. Then suddenly all the power is back. Then there are a few "power cuts" of a second or so and immediate restitution of normal power. Then another several minute cut of power with another restitution of power which lasted until I got to my friend's place. I'm thinking "bad gas" and the next day bought a can of Sea Foam, added half of it to the near empty tank, filled up the tank and took the bike for a 20 mile ride. Great power; no problems. Parked the bike in friends garage for a few days while we fished. (Not relevant, but yesterday caught three trout over 3 pounds - kept one - on the most improbable #14 dry fly fished deep on a sinking line!)
The first 120 miles of my trip home today were absolutely free of any bike problems. Then the loss of power returned, and stayed. Adding the rest of the Sea Foam and filling the tank didn't help. So I had something like 200 miles of rainy mountain pass riding on a bike that had something like a third of its 100 hp - always wondering if it was going to simply quit. Gear kept me warm and dry, but it was a scary trip. Did make it home.
A guy working at our place (former bike owner and one who had recently done some work on his old Volvo and failed to install one spark plug wire) suggested it sounded like the bike was running on three of its four cyclinders.
So, what say you about the plausible causes of the problems (and also the chance I've done terrible damage to the engine?) I'm thinking the most probable cause of the intermittent problems was not water in the gas but small grit which passed through the fuel injectors and, finally, a piece which blocked a single injector. But I know next to nothing about engines.
I clearly will have to take this bike to a mechanic - and it does still run, barely. Your advice would be most helpful if there are other possibilities which fit the symptoms described but have nothing to do with water or particles in the gas. That COULD have simply been a coincidence.
Thanks in advance for your thoughts.