I've seen them in person and not a fan. They look tacked on. I'd spend the time to restore the original trim on a set of used windows and then swap them on instead.
The quarter windows are what they call encapsulated glass. The molding is part of the glass. There are aftermarket replacements, but they don't have "Mustang" in them.
Mine need restored as well. I did pick up a used set that are in better condition.
I've heard Evercoat Poly Flex works very well on them. Then paint with SEM satin black.