Bob take it from someone who spent so much time in a water booth testing and fixing leaks at GM they thought I got water on the brain. You need to seal all interfaces otherwise water will get in.
Water has surface tension and will be drawn into tight crevices. Without sealer between the glass and gasket, water will wick right in. The shop manual has you use a sealer that is pumped in after the glass is installed to form a continuous bead around the outside edge of the gasket and the glass and again on the inside. You need a hand pump like an oil can. I have read of a guy who actually did it in a Ford plant. At home he took some metal tubing and flattened the end and stuck it over the pumper nozzle to create an nice narrow nozzle you could slip between the gasket and glass and pump in the sealer keeping it off the outside of the gasket.
You also need to seal between the gasket and the body. The manual calls out medium bodied sealer. You could use body caulk like the 3M stuff that comes in boxes of round beads which seems the consistency of the old stuff or 3M window weld which is Butyl and comes in ribbons and will seal fantastic but is messy. As mentioned in the manual make sure you take care to seal around the windshield molding clips, because the water can wick between the clip and the body and bypass the gasket and sealer.
Here is the shop manual instructions from 1961. The first two steps are to remove all the old sealer and then slip the gasket onto the glass.
As far as putting the sealer between the glass and the gasket first, I would not since you want it in the final position before you pump in the sealer to get a reliable seal. If you use sealer and the nozzle you should be dry as a drum and looking sweet.
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