It's a good idea to assess the condition of the holes in the header that you screw into. A lot of time this header wood is (at best) kinda mushy with age. With the windshield out is the time to consider drilling out the holes and inserting wooden dowels to give you some fresh meat to screw into. Don't do them all at once, leave several of the original holes so that you can line up the hinge with them to give you the location of the new holes in the dowels. Once you have the new holes located and drilled you can remove the windshield again and fix the last few you used as locators. Depending on how badly the header is rotted, I either use a small dowel and wood glue, or a larger dowel and epoxy.
When you put the new glass in, I find it handy to coat the rubber with a thin film of motor oil on each side, that makes it easy to slide into the windshield frame and the glass. The oil then expands the rubber to form a tight fit. I use a dab of black trim adhesive at the corners to seal the two strips of rubber to each other.
You might consider replacing the exterior rubber (around the outside of the three sides of the windshield) while you have the windshield off. This tends to get stiff with age and loses its ability to seal against the body. Don't use motor oil on this one, I use ArmorAll on the rubber bead to slide it into the window channel but almost any silicone-based product will work (like detailing spray or spray wax).