Months ago I had trimmed all of the windows to fit their respective cutouts. The windows all came marked with trim lines that I used my Dremel with a cutoff wheel to get down to. Each window was then sanded until if fit its cutout.
With the windows trimmed, I exposed a 3/4" contact strip around the edges and scuffed it and each flange. I then laid down a bead of LORD 7545 A/E plexiglas adhesive on the flange, carefully lowered the window into place and then used duct tape and weights to hold the window in-place while the adhesive cured.