Are you using digital voltmeter? If using analog[needle] they are at times very inaccurate. If using digital, 12 volts is dead battery. Fully charged battery after resting 12 hours will read 12.70 volts. When checking charge rate, at 3500 rpm should read between 13.5 and 14.3 volts. If showing near 12.0 volts, in all likely hood, regulator gone south.

You need to check all of the connections...again and then check them for a 3rd time. Also check and clean and clean the ground straps that go from the frame to the engine.

Have you upgraded the wiring yet with relays?

Once you have it runing with the volt meter attached, check the voltage at idle and 3500 rpm. let us know these values.