According to the "1966 Mustang Body Assembly Manual", there is no difference between the three body styles in the door windows except the glass assemblies, C5ZB-6321400-1, C5ZB-6521400-1, and C5ZB-7621400-1. All other hardware and unique Mustang designed parts are either a C4ZB- or C5ZB- (except the plugs in the trailing edge of the door).
Note: the glass assemblies are all 1965 assemblies.
I strongly recommend you get a set of "1966 Mustang Assembly Manuals", plus the "64-65 Chassi"s and "64-65 Weld and Sealant" - plus the "1966 Shelby Unique Parts Manual" (all published by Jim Osborn Reproductions).
Jim