I will try and answer your questions in order
Will this setup work with the stock r/r and stator?
In short, yes. I wired the stator and the R/R in such a way that I when I finaly did the MOFSET upgrade, all I had to do was unplug the OEM R/R harness from my new harness and make a harness for the new MOFSET R/R. At this point in time, I also made a plug inside the stator cover for both the pulsator coils and the stator, so I could change them out with out having to do too much extra work.
Also, how did you branch your cable runs? ie...same color running to multiple points. Did you multi tail terminal or cap/splice.
I started by running the longest run in the circuit. Starting at the Load (thing that power runs to) and going back to the power source (typically the relay that powers it, or the fuse). Then for the leg spliced in I would again start at the Load and run the wire to the most inconspicuous spot to splice said wire, cut wire to length. Mark where the two wires intersect, and cut the first wire at said spot. I then stripped the three wires bare, slid a piece of heat shrink tubing cut long enough to cover and seal the splice being made. I used a solder butt connector or solder y connector (depending on the angle and the direction the splice ran). I do not fuly understand your last question
Also, why the difference in terminal use on the ignition from your other setup with the stock harness
My stock harness was so badly hacked that I needed a new harness. SO I bought one off of a member here, but the harness he sold me was for an earlier model of VN7XX, it had some extra connectors, a few of the connectors were in the wrong spot, or the wrong shape... Over all in order for me to have made it work was going to require more time and effort than me just building one. Also I was having problems with my Junction Box, and my Ignition Box, so I wanted them gone out of the system as well. My new aftermarket ignition control box warranted a special harness any ways, so I just incorporated it into the system... even though the diagram above doesn't show it (both used pretty much the same schematic), only the new Control Box pushed out more juice to the coils, so need those wires beefed up to 12 gauge wire from 16 gauge wire.
I hope this answered some of your questions