Mustang body leaks aren't always rooted in the windshield and backlight. Cowl vents are the reason for leakage more times than windshields. Check your Mustang's cowl-vent dams for rust-through. Cracks in the lead seams at the roofline and A-pillars can cause a water leak. The same can be said for lead seams at the sail pillars and trunk area. Examine your Mustang's body thoroughly for leak sources. There are many, including rubber grommets around wiring harnesses, accelerator pedals, brake lines, and antenna leads. The rubber seal between the trunk lid and body will leak if exposed to substantial amounts of water. Quarter-panel end caps, taillights, side markers, and even trim pieces can be leak sources. Check them out.
Classic Mustang rear windows install the same way as windshields. Probably the most unforgiving rear window, also known as the backlight, is in the fastback. It leaks because it lies so flat, which makes it easy for moisture to collect around the perimeter and leak inside. That's why lots of sealer is needed around the fastback's rear window, especially around the outside between the rubber and body. Molding installation follows the same protocol: with a firm, soft hand.