I haven't yet done it but have taken one off. Its quite a job just to replace the window alone. You essentially have to remove the rear half of the top, take out the 500 staples from the bow that holds the top of the window panel, then put the whole top back together using a new curtain as its called. This is necessary since the curtain is underneath the rest of the top so water will drain over, not under the window. Where the bottom of the window/curtain attaches to the belt tack strip is the least of your worries. It would not surprise me that an original 44 year old top will not survive removal and re-installation of a rear window. A complete new top may need to be fitted since the material will be rotten and tear when you try to remove it. You might get away with re-using the top half of the zipper and mate that to the new bottom half of the zipper on the new window but I wouldn't count on that.
This link gives you an idea of what's involved in a complete top. They claim to be installing a CA Mustang top but it must be a non-original top since it says there is 4 1/2" between the chrome trim and the window. The Mustang windows I have seen go beyond the trim and are stapled directly through the clear plastic.
http://www.mustangmonthly.com/techar...top/index.html
The Ford shop manual has fairly good instructions but there are some errors in it as well likely caused by too much copying of instructions for some other Ford. Even though its fairly complete you have to study what the manual says for a few days, or take off an old top, before the words make any sense.
If you haven't seen one of these come apart or go together you need to do more investigation before you sign up for this job.
1965 Mustang Convertible Rear Window Replacement 
