I have a 2004 Ford Mustang convertible. My back

Glass is bonded to top cloth. You must replace entire rear cloth section and sew it to the top. Requires top removal and upholstery sewing machine. Farm this job out.

Salvage yard

This is a common problem. At the factory, the top material is bonded to the glass. That bond is breaking down. You can use Gorilla taps or urethane adhesive, but you will eventually need a new window unit.
The window unit is separate from the actual top. The top must be partially removed to replace the window unit.

Karl at aoksales.com

test for voltage at window motor plug. if there is voltage replace window motor. not a very fun job.

Installation of th e window takes special skills and tools. Please leave this to an automotive trim repair shop.

The dealer can fix virtually any problem with a late model car. But, if you use epoxy or trim adhesive, you may be able to do the repair yourself.

I once used 'gel' super glue to exactly meter and put glue where it belongs and get an instant bond on rubber to glass or rubber to metal bonding.

one side of the window attachment tract may have come unglued. you need an epoxy to reattach it.

This problem is very common and is known as delamination.
If the problem is not too far advanced, you can repair it with Urethane adhesive. It is used by glass shops to install windshields.
Your top and window unit are two separate parts.
If the problem is beyond repair, you will need to remove the rear half of the top and replace the window unit.

Karl at topgunwon.com

This is a professional job for a conv. top shop. has to be sewn in at the bottom.

Removal
NOTE: Mark vinyl to be removed so it can be returned to the same position after disassembly.

1. Remove sail area panels as outlined.

1. Remove staples retaining elastic straps at each side of back window glass (42006) to rear tacking strip and folding top rear number 4 bow (51278) and remove elastic straps.

1. Remove staples retaining rear bow corner pad (537A71) and bottom of folding top back window curtain (52500) to rear tacking strips.

1. Remove staples retaining top of folding top back window curtain to folding top rear number 4 bow and remove back window glass .

1994 mustang. don't have 89 Window, Rear Installation
NOTE: Transfer markings from the removed assembly.

1. Mark with grease pencil center point on folding top rear number 4 bow in line with hole on rear of folding top rear number 4 bow .
   

The window coming unglued is not an unusual problem for that car.
The bad news? To fix it correctly, you have to replace the top (like $2,500+)
I did automotive trim work (upholstery) for 19 years and have seen a number of problem with convertible top back windows (not just VW).
But because of the design of the top, the back window insert style, and the heated back window, they don't come cheap.
You can try taking it by a local trim shop (listed in the phonebook under automotive upholstery) and see if they have a "patch" fix they can do, but I can say, no patch is going to fix it permanently.
Sorry I don't have better news, but it is the nature of that beast.