I'd agree that using one of the programmable aftermarket units is the way to go. The stock FI components other than the ECU and the MPS can generally be used, and there's slowly getting to be a critical mass of people who've gone this route that you're likely to find someone who's been there to help with tuning.
CIS is actually a very nice setup for a turbo if electronics puts you off. I think at least one variation of the Type 3 or Type 4 used CIS/K-Jet (for a Bus? or was it the 912E?).
One that that's very helpful for the turbo fitter to have no matter what injection system you use, however, is programmable ignition control that can use manifold pressure to control advance. If electronics doesn't put you off, there are several Megasquirt related projects to include things like ignition timing and boost control directly in the Megasquirt unit.
See
Megasquirt forumsThe only real difficulty with MS right now is its very DIY nature, and the dizzying array of variations. Takes awhile just to figure out what's available.