This is basically what the factory used.
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1967 - 1973 Mercury Cougar / Ford Mustang Non-Hardening Glass Bedding Compound - New(Click Here for More Information or to Order)
Part #: 10022243
Price:$14.85
Glass bedding compound</td></tr></tbody></table>
Just make sure the pinch weld is clean and free of rust. I use the bedding and glazing compound as described above. 3M part number 08509. Most paint/parts suppliers will not know what your talking about is you ask for glass sealer. They'll try to sell you the urethane which you definitely do not want unless your windshield is for a '69 and above.
I'm dong the backglass on the '69 this weekend and will have 2 tubes of the 08509 on hand.
The 3M 08509 it what I have used several times. It can be messy, but not having leaks is more important in the long run. Here are the steps that I've used:
1) Tape the headliner really well.
2) Test fit the "S" seal around the glass to make sure it fits. I had a bad seal once and had to send it back for a correct fitting one.
3) Test fit a nylon cord inside the "S" channel for the pinch weld and have the ends meet at the bottom center of the glass. Remove cord.
4) Cut off the minimum amount off the end of the caulk tube tip and gently flatten it with a hammer.
5) Run a small bead of bedding compound down inside the channel of the "S" seal that fits over the glass.
6) Install the "S" seal around the edge of the glass.
7) Run a small bead of bedding compound down inside the channel of the "S" seal that fits over the pinch weld.
8) Insert the nylon cord into the "S" seal so that the loose ends meet at the bottom center, cross and have about 18" hanging out so you can wrap the cord around your hands several times.
9) Lay the glass in place on the outside of the window frame and have a friend push on the edge of the glass as you pull the cord toward you on the inside. Work your way from the bottom center around to the top center. The cord will pull the lip of the "S" seal over the pinch weld as you work it around the periphery of the glass.
10) Insert the flattened tip of the 3M 08509 tube inside the "S" seal and squirt as much sealant as you can, then squeeze out the excess and clean up.