First off I would remove the sash from the window and clean it up with a wire wheel, straighten it and paint it. I would polish the ends that travel in the side guides and get it smooth. That sash is in great shape compared to others I have fixed and replaced.
Reattaching the glass in the sash is no problem. You will need to thoroughly clean the channel and get some urethane adhesive caulk. Make sure you have the glass facing the correct way and glue it in place. I use some tape to pull it up in place and open or close the channel in the sash so it fits snug without adhesive in place. The old way of hammering the sash with a rubber wedge in the sash is dangerous and no needed. We have great adhesives today that can replace that method.
The rod will clip into a plastic retainer and should stay in place.
Something similar to these. Use oil and grease on the crank driver and regulator and clean the sash roller guides and grease them. Getting everything shiny clean and greased is key to keeping the rear window happy and operational. Spray lubes are worthless for this application and IMHO most applications. Good old oil and grease work best on the old vehicles that have lots of metal parts moving against each other. Good Luck and report back on your progress. I have a trim Lock material I use in the side guides. You can see my tailgate rebuilding in my Terminus M1009 thread. Take Care.