Jay-
How did you determine that the jumper wire is causing the fault in the charging system? I am unaware of anything else in that circuit that would do that, but if it makes you feel better, check for continuity between the white/pink wire AT THE CLUTCH SWITCH, and the stock wire at the relay. If you have continuity, just run your jumper wire from the ign sw START to the white/pink wire at the clutch switch. It is the first item after the ignition switch in that circuit.
Take care,
-Chris
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