My opinion.
The Ford gears are good, use them if they fit your needs.
I don't think anyone will be worrying about the literal part numbers on the gears of a restoration because that is not an area any judge will ever inspect...if they can get factory gears in good condition they might use them, but I don't think anyone will be paying huge money to attain that type of restoration part because you can still attain 3.91:1 gears to complete a restoration
The same with differentials, bearings, connecting rod and main bearing cap fasteners, and other internal items nobody will ever see...as long as the part works properly, and functions the same as the factory part (think new Detroit Locker as opposed to vintage Detroit Locker) things will be fine.
The best scenario I see is you trading the factory gears to a restorer to make things "just right" for a good aftermarket set you can use in your non-restoration application.
Again, just my opinion.