Also thought about carb breathers immediately (knowing the problem from KLR's CVK 41)
Also good to have a look at the fix used by most KLR owners. It uses a T - connector and branches the breather into two, one running up to tail and one down to side stand. The remainder of the original tube on the carb must run slightly up (towards carb). Water entering from whereever will always drain out at the bottom and not run into the carb.
If you search for KLR and T-mod you will probably find half a million pages with instructions
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