With the headliner and dash complete, I could install the windshield and rear window.
I did a lot of research on this and learned about the rope-in technique. It turned out to be fairly easy.
For my Mustang, I left out the calk since I will eventually remove the glass to paint.
The hard part was getting the rubber weatherstrip around the windshield. The slot for the glass is very tight and the rubber is stiff so my hands were pretty sore after. The first step is flipping the weatherstrip so that the short side is at the top edge of the glass and laying the strip out over the glass.
Next I pried open the glass slot at a corner and worked it on the corner of the windshield a few inches in each direction. Then moved to the next corner on the short side and then the opposite corner and the remaining corner, trying to keep the weatherstrip stretched evenly. I finished by working each of the sides in place. I had to use a plastic strip to pry open the rubber in places. It helps to pat the strip in place as you go along.
To install, I used a length of thin nylon rope and tucked in into place around the full length of the perimeter and overlapped a little at the bottom center (It may be easier to install strings overlapping at the top). I found that an old silicone tube tip worked to quickly pull the rope along the edge.
I started rope-in by carefully placing bottom edge of the weatherstrip and windshield into the bottom flange making sure it is centered and down all the way. With the windshield laying in place, begin pulling on the rope ends equally, slowly, straight out. I found the corners to be the hardest part due to stiffness of the rubber. After, there were a few places where I had to press the weatherstrip in closer to the flange.
I repeated the same for the rear glass -- the rear glass was thinner so the seal went on easier.
Be careful with the rear glass, I know first hand that it can easily explode into thousands of tiny pieces.
There are lots of videos on this. I thought this video was the most useful https://www.youtube.com/watch?v=w4igX1ZO5as