Welcome to the party!
That's a hell of a first post! You don't see this sort of thing everyday!
So, you are intending to weld up the lower crankcase openings for the water and oil pumps behind the clutch basket and associated oil supply passages through the transmisson shafts? Fugg it, just use JB Weld and cake that crap around!
That clackety-clack-clack clutch noise is totally worth it!
I wish you well with your tuning on getting the engine running on the old-school carb bank! I'd recommend a set of CV carbs as opposed to the really old vacuum slide ones! Go big or go home, ya know!
I don't foresee any tuning issues related to the fuel pump and feed lines, pressure fed airbox, traction control, ride-by-wire, quickshifter, etc. And that choke lever on the left clip-on will be SOOOO sweet! All your friends will be jealous! Just unplug all those sensors and the ECU will ignore them. Easy-peazy!
Have fun reinventing the wheel and stuff! I'll just plug in my laptop and twiddle around with some numbers in the meantime.