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You can check the stator wires easily enough with a ohm meter at the voltage regulator (VR) which is mounted up under the front left side the bike. Here is a video on how to check if the stator wires are good (earlier bike with VR mounted on rear fender).
I will suggest that the bike in that video has a BAD alternator stator, inspite of what the author says. (You might look to see if he has another video?)

He did not check ohms from the yellow wires to Ground. Any connection/continuity to Ground is BAD/Short circuited!
The AC voltage tests that he performed shows it. There should be ZERO voltage indicated between any of the 3 Yellows & Ground.

He should have tested AC Voltage between the 3 pairings of Yellow wires like he checked their ohms.
Looking for about 30 AC volts at/near idle and 40 AC volts or more @ 4000 rpm!

At least he started his testing at the Source, even if he got it wrong. :(
 

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The three yellow wires when tested at the regulator were 5v, 48v, and 7v. I have no idea if those are normal numbers or not, hard to find much info as KLR's don't seem to break down that often.
Did you NOT Read my post directly above? Your stator windings are FRIED!
 

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For clarity, there should be no continuity between ground and the 3 yellow wires from stator
That is correct.
Therefore there should be No Voltage (AC or DC) Indicated between yellow wires & Ground. That was his Error in the video, which you basically replicated. One YT video can lead one astray as easily as one GPS on the wrong settings.

With 48ACV on one leg (one third) of the system only, its no wonder the battery won't charge.
The 3 legs of the system can only generate about 17 amps maximum, so 1 leg of the system equals about 5.1 amps.
The headlight on High beam consumes about 6.16 amps, not counting the other lights.
 
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