First time I have heard of this problem.
You have to start diagnosis somewhere and to keep this as simple as possible, I would start the bike and run it for just long enough to heat the exhaust headers, then measure the temp. of all four to see if the bike is running on four cylinders or not. My guess is that you lost a cylinder, and this simple test will give you that answer: if one pipe is significantly cooler than the other three, or two pipes are cooler than the other two, you have lost one or two cylinders. The answer to that question will bring us to the next diagnostic step.
Speaking generally, it is very unlikely that anything is significantly out of adjustment or spec. because all tuning parameters of the engine are controlled by the ECU, and it is not likely one was damaged by water but left it in a state that it still gives a valid reading but the incorrect one. Much more likely that you would just have a sensor error. Same thing goes for spark and fuel injection; both are controlled directly by the ECU and would not be expected to be 'out of whack' and cause the bike to run so poorly. More likely you lost one cylinder to something like a shorted fuel injector or shorted stick coil, and the bike is running on three cylinders.
Another thing to try is to try to dry the bike with something like a leaf blower; if there is a puddle of water sitting over / around something, you may be able to dislodge / drain it enough to cure the problem.
After that, I think it is going to take a manual and some active component testing on your part to track the problem down.
The very best of luck going forward. These bikes have proven to be very robust so I think you have a quirk that should be <relatively> easy to find and eliminate.
Brian
Been a long time since I've posted OR had any kind of issue but here I am... Washed her for the first time in a LONG time and now she starts but won't idle and exhaust gets glowing hot and pops excessively.
I've been over every inch of everything I cleaned and just can't find anything that I loosened or broke. I'm at my wits end as this is my favorite time of year. Suggestions please??