The cut-out system that you describes will only add a ton of complexity without adding any real benefit. Turbo motors don't build boost unless the motor is under load, so while cruising you get the same mileage as you would with no turbo at all.
The problem with a remote mount turbo would be if you have a leak on either the exhaust side or cold side, it will be much more difficult to diagnose.
If it were me I would keep it simple. While not perfect, people have had good luck with the $200 ebay single turbo manifold setups. Buy a good quality turbo, and decide if you want to go the carb or efi route. With EFI you can use megasquirt to control fuel injector pulse width. A carb would probably be easier and cheaper, but you lose the ability to fine tune your system like you would with efi.