A bit tough to cut, just take your time and hold it firmly.

Scoring works but be absolutely straight, not as forgiving as paper.

Gluing, I recommend Testors Clear Parts Cement (available at modeling hobby shops).

A thought if you will: you could print your transparencies per normal and then laminate them (glue them as a detail) to thicker clear plastic for strength. You can either buy the heavier plastic, up to 1mm thick I have found so far or use old packaging from carryout or figures or whatever you find. I am doing this for a wall in my FL build.

I played a bunch with gluing transparencies in the thread. If you're going to try gluing transparencies to other transparencies, I highly suggest the use of some kind of cardstock strip between the two transparency sheets, to hold them together.

I haven't played with the Testors Clear Parts Cement that Outlaw recommends, though, so it may end up solving everything.

Good luck, and be sure to post your results (good or bad), and hopefully some pics!