EFI help needed, Wiring questions.

If my alternator is internally regulated and has a sense wire that goes to a 12v source, (either the starter relay or a distribution block to battery +) wouldn't that eliminate any overcharging caused by harness voltage drop?

Not necessarily depends on where you connect the sense wire. The original VR power/ sense wire is essentially connected at the white ballast connector you had in your hand, the "run" wire. By that I mean spliced in there or somewhere near.