I too am having the same issue riding in the rain, plus some.
While this does not sound like your issue, but I have a bad valve cover gasket. After riding in the rain about a week ago, I experienced the same performance and I do not have the VBAK kit installed. Now everytime I start the bike and let it warm up (3 - 5 minutes), the front cylinder starts smoking like a Harley. I've been told the engine sputtering maybe from riding in a bad downpour, instead of oil leaking, water was able to get into the engine.
Do not know if my leg is being pulled or not, but bike is at the dealer getting fixed now. I also may have a bad fuel system too. Bike runs out of gas between 1 and 7 miles of riding with the low fuel light on (roughly 100-110 miles on a full tank). They have not found that issue but a Yamaha tech stated the issue could be the feul pump could not be keeping the correct pressure and something electrical was made worst in the rain.
Good luck finding your Gremlin