I did conduct the resistance checks again while off the bike and same results.
Still showing a short between the white wires and grnd?
Rotor should be 5.25 plus or minus 10% according to Yamaha's book. So.... 4.725 to 5.775 ohms. Yours is low but within limits... probably getting close to the end of it's life... but still good. And... how accurate is your meter? Mines been calibrated for aviation work, so I trust it. A cheap Chinese.... not so much.
After reading your last few comments, just want to make sure we're all on the same page here.... your stator is part of the charging system. It sends an A/C current to the rectifier. Along with that, the TCI crank sensor is attached to the stator. Yes, that means the stator is used for both systems... but keep the two systems separated when thinking about or discussing them.... two different systems.
The rotor gets power from the regulator to create a magnetic field to excite the stator which creates the A/C current. So the rotor is part of the charging system too. On the rotor is the TCI trigger magnet. So yes, it's also part of the ignition system...but again, keep the two systems separate in you mind... makes it easier to troubleshoot.
You said at one point your voltage got down to 5V before you shut the bike down. That led me (and others I suspect) to believe you have a charging and or battery problem. If your stator winding's are shorted to ground, then you do indeed have a charging problem. And I'm at a loss to understand how you could get over 14 volts when you rev the engine if the stator's shorted. Makes no sense.
And if revving it bring the voltage up to 14+V, how did the batt. voltage get down to 5 volts? Again, I'm a little confused. At this point about all I can recommend is that you replace the stator and go from there. What with all the PMA swaps out there, a "wanted" ad should get you tons of em dirt cheap.
I know your main concern is the bike cutting out at 3-4K rpm.... but until you get the charging sorted, you won't know if you have an ignition problem or low voltage is causing that.