Okay Sam, thanks for that video.
One thing I am not sure about is why your white 6-pin R/R connector wires are different from the picture Rich posted of his white 6-pin R/R connector wires. Don't you both have T's?
Based on this pin-out of a 6 pin connector:
https://images.app.goo.gl/v3kPe4sGrhKHYp3n6
it appears to me that the typical pin layout of a 6-pin R/R puts the three stator wires together, while the other three pins represent the R/R power out pin, the R/R ground pin, and the R/R sensing pin. So the yellows from the stator go to the lower three pins of the R/R.
That leaves us with those upper three pins on the R/R. And the B/Y looks to be the ground.
I suspect the two red wires represent the power wire out and the sensing wire.
So here is how I believe the the other red wires (three of them!) function.
The smaller red wire that connects to your battery + post and goes into the main harness carries power to the fourth fuse down (labeled MAIN) in your fuse block.
(I don't know why it is a 10A fuse as it originally was a 15A fuse.) That MAIN fuse feeds power thru a red wire that goes up to the ignition switch. When the ignition switch is turned on, an Orange wire brings power back to the fuse block and powers the top 3 fuses (which were originally 10A fuses).
I assume the R/B wire that you show going from the fuse box to the center pin on your white connector and then into the center pin of the R/R is powered by the MAIN fuse so that the R/R can monitor system voltage. (I'm not sure that it is a good idea for the R/R sensing wire to be powered all the time - even with the bike off).
To prove this out, break out your ohm meter and put one probe on the R/B wire (your WIRE TWO) going from the fuse block to the center pin of the white connector and the other probe on the red wire that connects to the battery + post.. I would expect continuity, ergo: the R/R sense the system voltage! (all the time?)
The final red wire (the one you referred to as WIRE ONE) that goes from the upper left pin of the connector into the main harness is the R/R power out wire from the R/R. Within the main harness that power out wire is spliced into the red wire that goes from the MAIN fuse to the ignition switch (described above). That allows the R/R to supply power to the ignition switch (and the vehicle electrical load) and/or a convoluted path back to the battery + post to charge the battery.
To prove this out, break out your ohm meter. Connect one probe to the smaller red wire that connects to the battery + post and the other probe to the power out wire from your white connector. Should always show continuity.
So that's how I figure the PO had the bike wired. No guarantees !
Hopefully it will make it easier for you to go from the current wiring to the one that Nessium reccomends.
And I hope someone will come along and check to see if I maybe I made some wrong assumptions.