My Pegaso Trail (similar motor) has the same exposed regulator/rectifier connector (located in the belly pan). I simply cut the connector out, soldered the wires together, and covered in tape. Bike has never let me down and its seen a lot of water. I also removed the entire sidestand cut-off switch and wiring to prevent future problems here. I would fit bars or something to protect the exposed waterpump from a fall (Off-the-road has a nice protector) - I fitted Givi engine bars.

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Frodo
06Aprilia Pegaso Trail 650
New Zealand