Are you sure 12.9 isn't ok? It is charging if the voltage goes up... but also yamaha's of this vintage (sorry I don't actually have one, so I'm just guessing) probably have a 6 wire rectifier, which should sense the battery voltage and stop charging when the battery is healthy and full.
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Check that each leg of the stator is good by checking that each yellow wire has about 0.3 - 0.4 ohms resistance against the other yellow wires, and that none of the yellow wires have continuity to ground. If one leg of your stator goes bad, it can overtax the remaining leg(s).
Corrosion causes resistance, which creates heat and lower voltage. Are just the connectors corroded, or are the wires also corroded?
To clean connectors, I use DeOxit. Spray it on, then plug and unplug the connector a few times. If that's not enough, I use a soft, brass bristle brush. If that's not enough to clean the connector to gleaming, then I replace the connector.
Incidentally, it's common for motorcycles to barely charge at idle. You often don't hit a 13.2 - 14.4V cutoff until a few thousand RPM.
Are you sure the connector is the issue? I'd test the actual output, or simply the resistance though the stator.
Connectors are more of a go/no-go.
It's hard to measure the resistance of the connection as they're corroded and messy in the back as well - but I think I can get a 0 ohm reading from each.
I just measured the stator (I know, should have done it ages ago) and have ~35-55V on all pairs.
Double checked the battery - the 12.4V static drops to 11.3V running with the stator disconnected but increases to 12.9V with the stator connected. It's not perfect, but it's working. I'm just going to ride and see how it works out.
If your battery is at 12.4V resting, then it's no good. Charge the battery fully, then let it rest for 24 hours. The voltage should be around 12.8. The lower the resting voltage, the worse the battery's condition, and the more it will tax your charging system.
The bike hasn't been seriously ridden yet and the battery has been cranking the engine a lot while trying to diagnose issues. I'm happy that it still at 12.4 - but I understand what you're saying.