Depends on what type of restoration you're doing. If it's dead stock, leave the vinyl top. If you're modifying it in other areas, I'd remove the vinyl top which would make it more universally appealing.
I agree that vinyl tops look better on Cougars than many other cars. Nonetheless, I don't personally care for them, and would never put one on a car I planned to keep. (OK, maybe if it was a houndstooth top on a '70 with matching interior. Maybe.)
But you said for resale, and in that case, originality wins out.
I could be wrong, but as vinyl tops become an increasingly rare sight, given that the OEMs have pretty much abandoned them for several years now, I see them losing their "old folks car" stigma and becoming another vintage "feature" that adds character.
If I were keeping it-- no way I'd keep the vinyl - but if I were flipping it - I would put it back the way it was - but improve the cheezy way the factory did it....to elliminate later rust returning. Anything worth doing is worth doing right. I'd take good pics as I refinnished to show the work that went in. I think it will help with quality to show for your efforts.