The balance factor as you mentioned is specific to the motor. Not the trans. With a manual the flywheel could be matched to the balance of the flexplate if you aready have one (I would imagine any competant machine shop could do this
) I'm not sure about the bellhousing meeting up...C4...T5...are all 302 block the same bolt patern? HOPE SOMEONE ELSE CAN HELP ... but that's another story. If you order a flywheel for that year of motor 80s or 60s or what ever it will be balanaced correct. (either 50 or 28 oz imbalance, new or old respectively) With a manual trans there are other parts that will be rotating, for instance the pressure plate. When my motor was balanced last year the shop "balanced" my brand new pressure plate. All you'll need to do after that is make sure that the pressure plate is at 0 balance. Most often the balance of the pressure place isn't checked even when they are replaced by ford, so I wouldn't worry too much about that one, unless of course your intentions for the motor are to sing it like an elementary school choir after a helium gulping contest.
Good luck in your search!