No, the new wiring won't have the FOMOCO sticker on it, but why is that a problem? Nobody but you will know the difference. I have shown my 65 in several shows, and nobody has questioned why my wiring harnesses don't have FOMOCO stickers on them. The Mustang club of America rules do not specify that the wiring must have those stickers, so why are you concerned?
If it is a problem for you, then take the time and energy to peel off those stickers and place them on your new wires. I doubt you will have much success with that though, because those old stickers are brittle and will most likely crumble in your fingers.