Good analysis, Joe. If the bike can be started by any means other than the starter motor, then the electronic ignition is working. It won't fire otherwise.

I would be suspicious of the switches too.
Whichever switch it is wouldn't be shorted, though, or you would blow a fuse and/or have sparks. But rainwater--which is not particularly conductive--getting between the contacts could prevent making a good enough connection to complete the circuit. (An open circuit, in other words, rather than a short.)