First let me say fantastic workmanship cam! Very impressive detail work and a beautiful bike.
This is a big topic covering a lot of different things so I'll just weigh in on what I know.
I have built a dozen or so 2-stroke jackshafted bikes but no 4-stroke yet...
That is why I am in this topic ;-}
All my JS builds were with the bolt-on SickBikeParts Shift Kit and used the bikes gears.
3-Speed internal hubs, 7speed derailuer hubs, a couple manual NuVinci 170 bubs, and even a fully automatic NuVinci Dev KIt hub.
Though your custom version of permanently mounting a 3-speed hub to the bike frame is indeed clever it seems to be pretty time and skill intensive just to build, and even harder to service with 2 chains to me.
Granted it sucks on a single drive chain shifting system if the pedal chain breaks and you have to push it, it rocks being able to change your whole shifting system by just changing the back wheel and shifter.
My personal ride started as a JS'ed stock 48cc on a 3-speed bike.
It went to a 66cc motor, same tranny.
Then that full drive train to new NuVinci Fully Automatic CVT Dev KIt hub. It died.
Then to NuVinci 170 CVT, it was fantastic that I could keep the motor at any rpm I wanted with the hubs smooth 'no-click' throttle-like shifter, it seems like I was always shifting. That hub went another build that still runs great but be warned! I have personally seen a 50% failure rate with a powerful motor!
My ride now sports a Shimano 3-speed and I couldn't be happier.