I believe original Ford is the way to go for all window mouldings. NOS parts can be acquired through eBay, forum classifieds, and other parts sources such as www.allclassicmotors.com (I've been happy with parts I've purchased from this source, including the restored rear window mouldings I bought for my '65 Fastback).
If you have fairly straight original mouldings without too many blemishes, it would be worth having them professionally polished, or doing it yourself if you feel capable.
All of the "sources" are getting their repop pieces from the same Taiwan manufacturer. I've used the repop pieces on a couple cars and swear that I'll never do it again. The fit is not perfect. The big problem is the metal is thinner than what the factory used. Not damaging the repop pieces while installing them is a challenge.
Exactly which pieces do you need? I have some spares that may be better than what you have. I also have a pair of factory original drip rail mouldings in Ex. condition.
When I speak of sources such as All Classic Motors, I'm not talking about reproduction parts suppliers such as NPD, Mustangs Unlimited, etc. Forum classifieds, eBay, and All Classic Motors are original Ford/NOS parts sources.
Sorry for the confusion, I was meaning to steer him clear of reproduction mouldings.
Ah yes, the old windshield molding problem... I wrestled with that issue for about a month. The repro 65-66 front molding seems to work OK on my car. The repro fastback rear molding is terrible. The problem is that the big bends at the bottom of the glass are not the same as original (at least when I bought mine about a year ago). I finally found an original set and paid some guy a ton of money to straighten and polish it out. It's still not perfect, but if you look at a lot of original fastbacks like I have, you will find that many were not that perfect from the factory.
Look for nice OEM pieces on ebay. Polishing them is easy - I've had good results with Mother's Mag Wheel polish and a cotton buffing wheel in a drill. If they have larger scratches use 1000-2000 sandpaper to get them out.