I use 1/8 inch thick plastic stock from Home Depot, comes in different size sheets, 2x3 or 2x4 foot size works for most size windows (I have an Integra and it's a pretty big window). I trace the factory glass window and then cut out the plastic using a glass/plastic cutter, then grind/file the edges to take off sharp edges. I attach 2 smallish metal L brackets (carefully drill holes and attach with rivets) to the inside of the plastic window to allow it to rest on the top of the door so it won't fall down. I then attach 2 more L brackets to the top portion of the window (on the inside) to attach tiny bungee cords and attach to cage bars inside. Racer tape to the outside along the window frame top helps ensure the wind won't grab it out when trailering.
Victor