You should be seeing a peak voltage of 14.0 - 15.0 @ 4000rpm.
I think that your bike may have a weak alternator.
You need to test the AC voltage output of all 3 pairings of the Yellow leads disconnected from the regulator. Should put out about 35-40 volts AC @ 4000rpm.
You can also test the resistance between pairings ( 0.3 - 1.0 ohms) & resistance to ground should be Infinite (any continuity to ground it is short circuited, Bad).
Thanks for your reply. This may be very helpful. I retook readings and here's what I saw:
DC readings:
Polaris Regulator 12.9v at idle (around 1250 rpms), 13.7v at 2000 rpms,
15.2v at 4000 rpms.
Factory Regulator 12.4-12.6v at idle, 13.6v at 2000 rpms, 14.0v at 4000 rpms.
AC readings from stator:
10.35, 10.2, 10.65vac at idle, 11.5, 11.0, 11.5vac at 2000 rpms, 9.7-11.74, 10.9-11.9, 10.9-12.0vac at 4000 rpms. At 4000 rpms the AC voltage was bouncing around quite a bit.
What do you make of those numbers?
EDIT: Here is the resistance between each of the 3 wires coming from the stator: .7-.8 ohm, .8 ohm, .8-.9 ohm. There is no continuity to ground on any of those wires.