I'm sure Shane will chime in again but from what I've been told when you delete the vent window the integrity of the inner and outer door skin suffers unless you completely re-engineer the door contsruction.
There is a tab joining the inner and outer door skins. That must be removed and the door does loose some rigidity. If the car is a hardtop or converitble, then you now have a bigger problem. The glass is trimmed with chrome along the top and back of the window. The trim meets the vent window and with the vent window gone there isn't anybody that makes that (or any) trim to continue the look for the new 1 peice glass. Another problem is the door handle(at least on the 62-65) on the inside of the car is in the way for the 1 piece glass to lower all the way. Relocate the door handle means also custom making door panels for the relocated door handle. A sedan is do-able but not very easily.
i came this close .. to doing this and then chickened out.. hahaha... wish i would of done it now. shane didn't you have pictures of how you did yours at one point - someone did - i saw em... used factory door handle made the bar u-shaped inside the door on a hardtop this would be easier ... that car is so badass dude