When I did my door glass 2 years ago I discovered my locally cut replacement glass was not as thick as the original and the glass setting tape I had was wrong. I'd also had my window frames powder coated so all my dimensions were working against me to use the glass setting tape. My lower glass run channels had deep rust pits in the grooves too, which I sand blasted clean. I used Loctite PL (Pro Line) S30 Roof and Flashing Polyurethane Sealant to put it all together. Home Depot: $6. Like tinnerjohn said you need to center the glass in the channel so I used 1/4" strips of the glass setting tape spaced and wrapped around the glass edge for centering,
Spacers filled the channels with the S30
Filling w S30 and then eased everything together. I found that kerosene works great to clean up the excess before the S30 sets up (messy; wear gloves). And like HandyAndy47 said there are pros and cons to using urethane vs the setting tape (Lord help me if I ever need to try to get the frames off of a broken window glass). Also, I found this S30 stuff works terrific for filling in the gaps that develop in the corners of your windshield gaskets. Use masking tape to get the guideline you want around the windshield opening and then use kerosene to manipulate the S30 to get the profile needed as the S30 begins to set.
Fix for shrunk w-shield gskt. By my picture you might see it's not perfect but it keeps the water out and looks better than a badly shrunk windshield gasket. Very few people have ever notice my repair. Good Luck. Dave