Has anyone ever had problems with their Stratoliner becoming waterlogged and failing to start after sitting out in a rain storm?

 I have a '14 deluxe that I rode 400 miles to Florida without a hitch. Parked it outside the motel, there was a rain storm during the night, and in the morning it failed to start. In fact, thought the starter would engage, it wouldn't completely turn over. I tried to jump it off thinking the battery was weak to no avail.

Leaving the bike for 24 hours, I went back and tried to crank it again. It turned completely over and eventually started. However, it ran poorly for the first 15 minutes after which it ran normally. All this has been puzzling.

I have however arrived at a diagnosis that I'd like someone to commit on. I'm thinking that my air box became waterlogged and the excessive water effectively locked the motor up. Then when it evaporated, it started.

I have Ivan's air box modification and have completely enjoyed it's benefits. Never have I before had any issues before ridding through rain or shine. Wonder if my prognosis seems plausible?

FYI, I'm not removing the air box modification even if it's the cause. An excellent mod.

Has anyone ever had problems with their Stratoliner becoming waterlogged and failing to start after sitting out in a rain storm?

I haven't had it fail.  I have had it be difficult.

Is the air box under the tank like the Raider? If so there shouldn't be any water getting into it - water would not cause it to not turn over - sounds more like you need to check all of your connectors that might be exposed to make sure they are staying dry. Since you said after letting it sit it ran leads me to that conclusion.
If water was able to get into the air box while the bike is sitting still then it would be worse if you rode it in the rain 

This happens to me every time there is a heavy rain. Light rain or washing at the car wash doesn't affect it. Haven't had any luck with a solution.

Interestingly enough, as a follow-up, when I changed my oil shortly after this event about 8 ounces of water came out of the oil pan.  Scary huh! Bike appears to be running fine though. Apparently all the water collected on the bottom. Never did have that typical milky look to the oil.

Wow, that is scary.  Well, the airbox does connect to the cylinder head breather.

I have a cover and keep it covered if it's to be left outside which is rare. But the lesson I had to learn was to make my wife leave that 1 extra change of clothes while traveling and instead take my bike cover...:-)

LOL