Make sure you get all the old sealer out of there. If it's the original stuff, it's probably pretty hard anyway. That entire area is prone to rust because the sealer breaks down and water gets under it. Make sure you remove any rust with a wire brush or wheel.
I've had some pretty good luck with a product called Aero-flex. It's a seam sealer that comes in it's own dispenser so you don't need a caulking gun. You can use it in many places on your car as you restore it. It adheres really well to the metal and it's paintable. Although the directions say you can paint over it in an hour, I always waited 24 hours before priming and painting. Whatever product you choose, make sure it accepts paint and clear coat. Good Luck. :winks
Urethane caulk will work. It's cheap and available at most hardware stores. Keep some paint thinner (use sparingly) and a small brush handy to smooth any rough edges on the roof side before it dries. Before you start, consider what you'll use to spread it. Fingers don't work well in such a narrow channel.
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