OK, so there are ONLY 4 normal ways for anything to get into the cylinder, these are as follows, via;-
1. The Valves
2. The Spark Plug
3. The Piston Rings
4. The Head Gasket
5. Crack in head or cylinder (not normal)
So working in reverse order we can exclude certain items. Head Gasket, would either consume fluid & the caught fluid would be coolant, or it would over pressure the cooling system &/or produce white smoke with the engine running. So not likely. Same for number 5, you would experience other issues probably !
Piston Rings, when on centre stand the oil level is just below the water pump shaft hole, when on side stand even with piston at BDC on #1, the level is NO WHERE near the base of the piston, thus the crankcase would need to fill with water to come up past the rings. So not an option.
The Spark plug, is generally a sealed item once located, so unlikely to be an issue. You would lose spark if the plug itself was leaking & you would experience blowby marks from combustion if it was loose, as well as damp on the plug cap sides & in the plug tunnel.
That leaves the valves, which strangely are where stuff is supposed to enter the cylinder from. As the throttle bodies are under the airbox & that is under the tank, then generally this area is shielded from water. Except for a few areas !
The tank filler has a drain/overflow which is connected to a stub under the tank front right on 5th gens, assume same on 6th & later.
If that stub does NOT have a hose attached &/or if the hose is blocked, then it will leak water onto the top of the airbox, around where the snorkel fits into the airbox.
If you have removed the snorkel & the bike is on the side stand, then this water could track along the inside of the airbox lid, following a gravity path it would meet the cross lid reinforcement & then potentially drip in the rear left area of the airbox. If you have a standard filter this would pass through the filter & may drip directly into the velocity stack for that cylinder ! Which is #1 at rear left !!!!!
The other areas, are drip into inside of airbox then runs across floor of airbox & seeps around outside of velocity stack into the #1 cylinder throttle body & into the cylinder. Alternately, if the airbox is NOT fitted properly, this water could track around outside of airbox following a gravity path to the rubber TB isolators that link TB to head, if the airbox, or the TB clamp is loose, then water could seep into the intake on #1 cylinder.
I'd expect it to be the first of these two as the issue. Can be determined, by lifting tank & opening airbox after a period of rain ! Use a chammy to dry the excess water off the tank before lifting to ensure only rain that has got there before you leaves wet marks.
As far as the PAIR suggestions go as an access point, it does not stack up, this is under the tank, you would detect wet around the PAIR head cover. Assuming PAIR is still enabled/attached. But it is an option for a water access point. You could always go as far as TDC/BDC parking that cylinder so exhaust or inlet only is open or neither & see what happens then. If PAIR exhaust will have water in it, if intake & valve seal is good, then water will appear below butterflies !