There's something dodgy inside that box then. What exactly is this box? If you are testing diodes inside it, is it the regulator/rectifier you're talking about? upload pix and or a pic/scan of the relevant item in the wiring diagram.
Also, to help pinpoint the problem you could put the bike on a stand or loosen/remove the chain or something similar so that you can put it in first and let the clutch out without the bike moving - then you can wiggle things away and watch for the bike to die.
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