The glass in the back has moved and the vinyl holding the glass on the bottom of the glass is not connected and wind is blowing in

Pull your door trim off, they are mostly clips but there are screws holding the arrest and door handler, the window winder has a half-moon clip at the base which is a bit of a struggle to release without the correct tool (angle point nose long nose pliers worked for me a long time ago) remove the glad wrap plastic dust cover and any remaining broken glass from the rail, put the win wiper down about half way. Slide the new glass in from the cab side and position it into the rail and wind it down all the way, now position the new glass into the door guide slots and carefully wind the window up and reposition the glass while winding it up and down making sure there is no resistance and when your happy put the door back together. (ripped the plastic/gladwrap dust cover up didn't you, that black chewing gum is a *itch eh?).

Hi,
You'll need to take off the door card
& undo the screws or bolts which hold the rear window rail/guide in place at the bottom.
Then, wind the window down, whilst supporting the glass from underneath.
Once it's low enough, you should be able to re-align the glass into the two rails/guides.
Wind the window back up, taking care not to let it jump out of the guides.
Secure the screws or bolts which hold the guides in place, before testing the operation of the window.
Once you're happy with the job, reassemble the door card.

It is important that you discover why the window came out of the guide in the first place, or it may well do it again.?
Check the stability & security of all the guides, screws or bolts & drive or winder operation, whilst the door card is off.

Best of luck

remove the door trim and adjust the window channel to hold the glass square . there will be screw adjustments at the bottom of the channel for this . wind the window all the way down and push the channel against the glass then tighten the screws

remove the door trim to get to in side the door. One of the glass tracks will have an adjustment on the lower mount where you can move the track in or out depending what you want. Normally wind the window right down and adjust the track tight against the glass( make sure the glass is in straight). wind the glass up and down a few times to ensure that there are no tight spots Some spray silicon in the tracks helps with the movement of the glass.

You may have to review notes on how to remove the drivers side panel and replace one of the broken screws that hold the glass in place on the bottom rail. I believe the cause my be that and if not it may be a sticky guide rail. Try rubbing some furniture polish on the edge of the glass that sticks (usually to opposite side of the one that does not match the door). This may help to get the glass sliding smoothly again.

honestly I would replace the whole regulator

its come off the track and hold down inside the door , remove the panel inspect the window glass at the bottom, some have holes in them that a vinyl insert clamps to, and others are secured with only a double sided tape,, one or the other of these has come loose

Jeep Wagoneer/Commando/Cherokee 1984-1998
Sunroof - Removal & Installation

1. Remove the wind deflector mechanism covers.
2. Position the glass to the vent position.
3. Position the sunshade full rearward.
4. Loosen the nuts holding the glass panel to the side adjustment brackets.
5. Slide the glass panel rearward 0.50 in. (12mm) and separate the glass from the sunroof unit.
   

To install:

1. Position the glass panel in the opening with the logo rearward and slide the panel forward 0.50 in. (12mm).
2. Verify that the attaching nuts are below the top surface of the glass adjustment brackets.
3. Close the sunroof to center the glass in the opening.
4. Tighten the center screws to hold the adjustment.
5. Open the glass to the vent position and tighten the nuts to 71 inch lbs. (8 Nm).
6. Close the glass and check the alignment.
7. Install the mechanism covers.
8. Adjust the wind deflector if necessary.

Hope helps (remember rated this).

Remove the black vinyl trim from the edge of the glass. Remove broken glass & urethane adhesive from the metal pinchweld leaving a thin layer (approx 1/16") of urethane for new new urethane to adhere to. Vacuum broken glass. Prime nicks to the metal to protect from rusting (also insuring a good surface to bond to). Attach vinyl reveal molding to glass (unless it's a "T" shaped push in type - it would install after the glass is set). Clean and prime the replacement glass. Apply new urethane adhesive. Set glass in place.Slide the metal joint cover in place on the molding (at bottom in the center). Clean outer surface of glass. Allow for safe drive away as noted by urethane manufacturer.

well I went to Lowes and shopped for a construction adhesive. I picked PL brand Polyurethane Premium Construction Adhesive because it is (so they say) 3 times stronger than ordinary adhesives.
It is also water and weather proof
Bonds to wood, metal, stone, concrete, masonry, bricks, vinyl, plastics
It came in a tube (you know.. chaulking gun style)

How could it NOT hold glass to fabric??? Thats what I said to myself.. well when we have nothing to lose, we'll try anything.

I put a good bead about 3/8 of an inch in between the glass and fabric, waited 7 days and then razored the excess off the glass. Applied black permanent marker and I'm done. So, it's been about 2 weeks and it's holding well so far.
I'm a betting man, but I won't bet this is going to hold... would you?