There are mysteries that have perplexed mankind for centuries. We're going to leave these issues for greater minds and focus on more recent mysteries, such as what to do about leaking windshields and backlights. We could suggest visiting a reputable local glass shop. However, we've learned most windshield shops today don't know any more about replacing vintage window glass than the average garage-born-and-raised enthusiast. We've seen all kinds of careless installations performed by so-called professionals. We've hired local glass shops that guaranteed a leak-free installation and still wound up with water on our feet.
Proper installation begins...
Proper installation begins with new trim clips from any autobody supply store or AMK Products. These trim clips are zinc-coated to prevent corrosion. It's more challenging to install them when you're dealing with a vinyl top. We suggest new clips because you want them to adhere to the pins and trim. When pins have broken off, use a button-head Phillips screw (like you see on kick panels).
So what should you do when it seems few windshield replacement professionals have the expertise to properly install vintage Mustang glass? Our suggestion is to do it yourself, following some basic guidelines that date back to the way Ford assembled these cars. We've found windshield professionals use either too much or too little windshield sealer. They also use the wrong kind. What's more, they apply sealer where it was never intended to go. Some shops use no sealer whatsoever and slap the trim back on, hoping you'll never notice.
The best anti-leak suggestion we can offer is to follow your Ford Shop Manual's instructions to the letter, applying sealer exactly where Ford tells you to, and increase the dosage for extra added measure.
Windshield Sealer
You have a couple of windshield sealer choices for classic Mustangs with rubber gaskets. Adcobond R-900 from ADCO Products is the most appropriate windshield sealer, available at most autobody supply stores. It's the nastiest composition you have ever seen, but it seals like nothing else. Here's a word to the wise: Don't get R-900 on your hands or clothing. It will never come out of clothing, and lots of lacquer thinner will be needed to remove this sealer from your hands.
If you can't find R-900, opt for 3M's Windo-Weld Resealant #08634, available anywhere 3M products are sold. Windo-Weld has a similar composition to R-900 and seals just as well.

Use a trim removal tool, available...

Use a trim removal tool, available at any autobody supply store, to drive windshield-molding clips in place. Using a screwdriver, chisel, or gasket scraper can cause distortion.

Windshield gasket preparation...

Windshield gasket preparation is everything to proper installation. When you install the rubber gasket, use a soapy solution for lubrication. Lubrication at the glass groove is necessary for easy installation. Install the gasket rounded side out and with the shortest length on top.

Don't apply sealer in the...

Don't apply sealer in the grooves. Run a bead of sealer around the seal's outside perimeter where body contact will be made. Using sealer in the groove causes a very messy installation and accomplishes nothing.

Before the glass goes in,...

Before the glass goes in, the surfaces must be clean. Kendall McSparren of McSparren Auto Glass in Stockton, California, stresses the application of a good windshield primer to surfaces before installation, which improves bonding between rubber and paint.

When you lay the window glass...

When you lay the window glass and gasket in place, you have to have a way to pop the lip inside for security. This is why we use a rope (lawn mower engine starter cord is perfect) inside the outer groove as shown. Position the ends at the bottom, where they're easily accessed and pulled.

The windshield/gasket assembly...

The windshield/gasket assembly is squarely positioned and gently pressed against the frame. Again, we can't stress enough that the surfaces must be clean and primed with windshield sealer primer for good adhesion and sealing.

Press the windshield/gasket...

Press the windshield/gasket assembly into place. While pushing on the glass, the rope is pulled both ways to pop the gasket lip inside. It's a good idea to use a lubricant (soapy water) in the outer groove for a smooth transition. Make sure the lip is evenly popped for 360 degrees. No wrinkles in the gaskets are allowed because they cause leaks.

Run a bead of R-900 or 3M's...

Run a bead of R-900 or 3M's Windo-Weld around the perimeter once the windshield has seated. Make sure you have wall-to-wall sealer from gasket to body. This is where windshields leak most--between the gasket and body. Fill this area in to eliminate the potential for leaks. When you install trim, you seal it up.

Kendall suggests a bead of...

Kendall suggests a bead of R-900 or Windo-Weld between the glass and gasket to further eliminate leaks. Leaks can occur at trim clips, which is why you want sealer between the clips and the body--and at the base of the clip.

Backlight installation isn't...

Backlight installation isn't much different from that of the windshield, and it's virtually impossible to get the gasket backward. Install the rear window gasket as shown, using soapy water as a lubricant. The wide part of the seal goes to the inside bottom at your package shelf (inside glass radius).

Windshield trim is installed...

Windshield trim is installed next. Reproduction stainless trim is more challenging to install. Where possible, have original factory trim repaired and polished because it is much easier to install. Begin trim installation at the bottom, then side trim, and finally the two top pieces.

Sealer is applied at the outer...

Sealer is applied at the outer perimeter corners where body contact is made. Fastbacks are notorious for rear window leaks. This is why you want to be generous with sealer between the gasket and body. Pile it on thick, then allow it to settle before applying a final bead and trim. Clean up with lacquer thinner or a petroleum-based professional glass cleaner.

The backlight is positioned...

The backlight is positioned with the bottom lip seated first.

The glass is pressed into...

The glass is pressed into place and spanked. With pressure applied, the rope is pulled to pop the inner lip. Once the window is seated, spanking continues to fully seat the gasket. As with the windshield, sealer is deeply applied to completely fill in that vulnerable area between the gasket and body. Install trim.