After I greased all the plugs,I bought a box of 3M black strip caulking and wraped it around both sides of all the plugs where they go together,where the wires come in and out of the plugs,and all the joints for the snorkel in and out lets. I ride up,down and across a river all the time. I have been in so deep the seat came off and started to float down stream. Have never had a problem since I did these 2 things.
Check harness for bare spots ... I didn't believe I had any bit after close inspection I found spot on steering stem. Also a yellow plug under there that is supposed to not be sealed well ... If memory serves me right
Do not use tape. Electrical tape holds water and moisture. Use the 3m strip calking.It is water proof,tape is not. Tape will let water get past and hold misture and cause corrosin on wire and connectors. I was a mechanic for Penn DOT on the plow trucks. Any time some one used tape I had a wiring night mare. You can use rtv sealer from a can or tube,but if you have to get it off all the way to get at the wires it is almost impossible. The strip caulk can be pulled off easily by hand,and anything left can be taken off all the way with brake clean,carb cleaner,kerosene, diesel and if all you had and were really carefull.... You could use gas. Of course I do not recomend gas. The caulk has worked great for me.
From the sounds of it you are running the stock intake and no snorkel. Right? If so, Steam from a hot exhaust and engine could be addint to your problems. They don;t run well and often die when steam is sucked into the air intake.
I had an NGK spark plug go bad on me once. It started stalling in deep water and by the end of the day would die in a puddle if the water splashed up on the plug wire.
Change the plug so you at least know whether that's it or not.
Dielectric grease in every terminal including the fuse plugs will prevent corrrosion issues for sure.