Eric, There are a couple of other issues to deal with beyond what you mentioned. The main one is the engine control system. Many installations use only the TPS (throttle position.) This is not to say that they aren't capable of other inputs, but most realworld applications are that way. Some have used individual lines from each TB (throttle body) into a manifold from which a composite manifold pressure is read. There are those who say this does not supply an adequate representation of manifold pressure to provide a load factor into the injector timing and duration outputs. There are various schools of thought on this and I am not advocating or deriding any of them. Individual TBs/runners are, to me, the ultimate in cool on a GT40, BUT educate yourself well on the alternatives of ECU systems out there to make sure the assumptions and compromises will provide the driveability you can live with. Kinsler's catalog has a very good matrix of ECU systems available and their capabilities. There are other types out there beyond what is listed, but this is a good starting point. The guys at Kinsler are racers who were very straight with me when I talked with them.
If you chose to use stock type EFI do keep in mind that the '94/'95 upper intake will be needed to fit under the rear deck on a 302.