Window is separated from the top.The window is not broken. Top is in good shape.

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

For 300 bucks you can have a new top WITH a rear glass window. It's really not worth messing with for that price. Otherwise, consider Duct tape. :(

is there a rubber bushing between the trans and mount. make sure this is secured properly.

Your glass was originally heat sealed to the top material. When it begins delaminating, your only recourse is to replace the top because your new top will come with a new window. Any sticky gooey repairs are very temporary at best

Good luck, Karl at aoksales.com

that has to be sewed in

The rear window in your car is a separate part from the top so it can be replaced without replacing the top.
You must, however remove most of the top.
Windows are available on Ebay and instructions are available on DVD here.
http://www.topgunwon.com/DVD/

Regards, Karl

Your window is not attached to the top material.
Both the top and the window are attached directly to the frame.
You can get instructions for this procedure on DVD at this link.
http://www.topgunwon.com/DVD/

Regards, Karl

Look for a junkyard around that sells the window or buy one online for dirt cheap and then put it in yourself. It is not that hard just time consuming.

This problem is very common and is known as delamination.
Use Urethane adhesive to reglue the window.
This same adhesive is used to install windshields.
The hard part will be to hold the window in place till the Urethane cures.
Prepare for that in advance.

Karl at Topgunwon.com

Pull out window crank and door handle, remove panel, remove plastic Nylon that's between metal and panel, crank the window down enough to see the arm and the part that connects with glass. Make sure the metal part inside the door that comes from an arm and attaches to glass is clean, from broken glass and the gap that attaches to window is clean,bend the new glass to make it fit inside the opening slide down the new glass from the top using opening guides, grave it from both sides standing in between and make land on top center of the part that graves the glass, put automotive glass silicone on center of that part,just at where graves the glass, let dry, put the plastic back the door panel the window crank with the "U" shaped lock washer and the door handle, I hope I was clear