My vote would be for a fully programmable EFI all the way. It just opens up so many more possibilities. For instance, you could mount a flex fuel sensor and run E85. Or if E85 isn't readily available where you live, you could also install a good quality methanol injection kit and drive it with the EFI. Either can net gains of 20% - 30% on a forced induction engine because of the increased octane and charge cooling effect. If you're not running really high boost, there's a possibility you may not even need an intercooler, which would simplify your plumbing.
EFI would give you many other options too, such as boost-by-gear, knock detection/response, closed loop fuel adjustment, closed loop boost control, etc. etc.
I love your ambitious plans. Someday I want to do something similar for my 68 Newport, so I'll be following your progress for sure. In my case, though I'd love to go turbo I think the plumbing would be too challenging so I'd probably go with a radial supercharger