Hopefully you can provide more information on adjusting the door glass as you mention above. The front edge of my passenger window glass slips out the the nylon door glass guide in the vertical quarter light frame/post. Also, the rear edge of the window is not being lifted as high as it should be lifted.
Bill, is the nylon guide (Moss #86) in good shape, held in place securely, not broken or worn down so it doesn't extend past the glass channel (Moss #111)?
If worn replacement is needed. If ok, then the quarter light track may need adjustment or the track channel is too wide. To test the U-Track channel width is consistent, find a socket end that will fit inside the track and slide it top to bottom in the track. If it binds up and stops, widen that area (I used a pair of pliers, ends wrapped in tape, by inserting and pulling apart). If it's too loose, squeeze that area closed a little (Pliers). Once confirmed the track width is correct, if the nylon guide still comes out, adjustments of the quarter light assembly is needed. Remove the door waist molding (held in place with dum dum or some sort of pliable sealant). The waist molding front edge has been bent so as to make a U-shape. Pull the waist molding straight up. Some wiggling or moving it forward/back a tad may be needed. Once off you should find 1 or 2 screws are used to hold the top plate of the quarter light in place. Remove those screws and loosen the screw (Moss # 168) at Vent Window To Door Bracket (Moss #164) attached to the bottom of the windows track. Now you should be able to adjust track angle front/back. You can adjust the window angle out a little (where it meets the top) by adding shims (washers) under #164. If the glass is pushing inwards too much, adjustment is made at the top.
You may need to adjust the rear window track too. There are 2 small nuts (on the outer edge of the rear door). One at the top one at the bottom. Loosen those and adjust the track inside the door. Both tracks may need adjustment, because the window tracks are curved, same as the widow. So adjusting the front or rear alone may now make the window bind because the curve of the windows tracks are not parallel.
As far as the rear of the window not being lifted as high as the front, that maybe a top fit issue. The glass has a metal window frame, which has a Regulator To Channel Bracket (Moss #84) on the bottom of the frame. The glass movement up/down is adjusted by the Window Winder Assembly (Moss #100) which slides in #84. The height stop is made by the Stop Door Glass Bracket (Moss #93). It does not allow glass angle adjustments, only height. If someone replaced the glass and didn't install it correctly in the glass frame, that may account for your situation, but I doubt it.
Please put the top up, clamped in place. Roll the widow up and take some photos of the gap along the entire glass edge to top. It may help to remove the rubber seal to show the gap better. I'll provide examples of my top to glass edge. 1st photo is with the rubber seal in place.