I just went through that "gluing" exercise myself. I had the same question you did..... "what is the exact position of the guide?". To find this position, I rolled the window up and then put the guide around the window in the spot where it would not limit the upward movement of the window. As I recall, the bottom of the guide ended up being about 1/4" from the bottom of the glass.
I'm interested in what you use for the "glue". I ended up using a Permatex RTV material. I took out the felt, cleaned the glass and inside of the guide and filled the groove with RTV. Then, I shoved the guide onto the glass, wiped off the excess RTV and let it set up. The next day I could not budge the guide, so I installed the window. It has been good for 2 months now.