The '69 glued in windows were NOT one of Fords better ideas. The best fix is to use mechanisms from a '70 model 'Stang. Replacement with that assembly is the preferred, long term fix. If that isn't possible, any reputable glass company should be able to recommend an adhesive that might work.
65 Hi-Po F/B
67 GTA F/B (small block)
MCA 27479
65 Hi-Po F/B
67 GTA F/B (small block)
MCA 27479