Silly question, but I have to ask....
Are the wires you're replacing the same gauge (size) or bigger than OEM?
I'm sure you already did, but also look for any chafed/pinched wires, or burn marks from an elec arc.
If it was water that seems to have started this issue, maybe disconnect all your elec connections, make sure it's dry and add some dielectric grease to them to keep water out.
By doing that, I'm hoping you will inspect all of your elec system and maybe find the source of your problem.
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My Yerban assault vehicle: 2.2mm stroker crank, 62mm Nikasil cyl, Taida large vavle head, American made valve springs, ported intake manifold, TM 28mm carb, stock CDI, Bando coil, TK exhaust, stock CVT except for the 14g sliders, 13/40 internal gears, 16T drive, 31T axle sprocket, 22" rear tires, and ONE BIG POTATO CANNON mounted on top..........
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