I'd call your local glass place and have them do it. But you'll want to take the tracks out and knock out all of the old junk. I took me a couple days to get the tracks cleaned up, then I called the glass store. They sent someone to the house and glued them both in for $50. I hear a lot of people having trouble with the windows coming un-glued. I've never had that problem.
I used silicon RTV on one window when it ceremoniously fell out, it is in there solid now, glued about 1/4" too far back. The trick to lining these up when you glue them in (I found out after) is to run them all the way up when they are drying, and if need be tap them back or forward as needed.
69 Sportsroof, 351C, 4spd toploader, Restomod BOSS 429 clone - the one and only (?) 1969 BOSS 351
I included one of my responses to a similar question from the old forum at the end of this response. First I used a bit of masking tape to mark the position of the glass in the channel. There will be two adhesives on your window channel. A rubbery one and a hard epoxy type underlayer. I removed all of the rubbery stuff and thouroughly scuffed the hard epoxy layer using sandpaper wrapped around a paint mixing stick. On the window I used I cleaned most of the adhesive off the window except for a very small amount under the tpe that I used to mark the position of the glass. I then used the 3M channel bonding and sidelite adhesive available from Mustangs Unlimited to re glue the window in place. I set the window upright between blocks and allowed it to dry in that position. It has been about a year now and everything seems to be holding together well. There's a link to the 3M site in the portion below...you can use it to check out your options.
What 3M part number are you using? Is it the #08641 Channel bonding and sidelite adhesive?? If not maybe you could try it. If you perform a search on this site someone suggested using rubber tubing around the base of the window guide rods to act as a stop...The theory was that the reason the '69's have problems with windows popping out of the channel is that the lower stop strikes the middle of the glass (on that little metal striker plate) and pushes it up out of the channels...by using rubber stops around the guide rods you transfer the stopping force to the channels themselves eliminating upward force on the glass...I haven't done it but it made sense to me. As far as the epoxy goes, I don't think that there would be a problem, but then I don't know why 3M would not endorse their epoxy glass adhesive (http://products.mmm.com/us/auto_mar...wurl=CMQNKYH4beLPLPKL4XgeT1T4S9TCgvTVVYT3Q5gl)
for this particular purpose... The only other thing I can think of is glass and metal prep prior to gluing that may affect your results like using a petroleum based solvent like acetone to clean the glass. You may try a good scuffing with an abrasive cleanser like comet then rinsing well and drying thouroughly with a solvent free cloth to clean both surfaces.