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The problem is almost certainly electrical. It is unusual for water to affect low voltage circuits (12 volts) but water can cause havoc with high voltage circuits -- think coils, plug wires and plug caps. It is very characteristic of high voltage problems to cause rough running and stalling at low rpm but let the engine run acceptably at higher rpms. This could be a difficult problem to track down.
Plug wires can crack, plug boots can get torn and coils do crack. When that happens the high voltage will jump from the defect to ground, bypassing the spark plug. One thing you can try is fairly easy. Raise the tank, take off the heat blanket, remove the rubber shield under the Tee bar (my Gen I has a rubber shield, dunno about the Gen II) and expose the valve cover. Inspect what you can see and reach, look for cracks and chaffing at wire contact points. Check that the plug caps are firmly attached and look for damage to boots. Find/buy a spray bottle that can make a fine mist. In the dark, with the engine running, use the bottle to mist the plugs, plug wires leading to the coils and the coils. If any of the high voltage components have a problem you will almost always see lightning bolts. Unfortunately, the way the coils attach it is possible for a coil to 'leak' high voltage to ground without your being able to see it. In any case, when you mist an area and cause an arc you should notice the engine speed or engine smoothness to change. Spraying one area at a time will help pinpoint the problem.
