Dip the windshields in Future floor finish (yes, you read that right). I laughed when I heard of that, then saw the results, now I'm a believer! It should fill in fine scratches. If your cat hates you and really scratched them up, you will have to buff them. I dip all my clear parts in Future now. Once I get an airbrush it will become my clearcoat of choice. You can even tint the future first to get that tinted glass look. See Swanny's website for tips and tricks on that (http://www.swannysmodels.com/Tinting.html). You'll want to bookmark his site as an invaluable aid. Same with MusicCity's (http://www.craigcentral.com/models/). There are plenty of threads on the forums about Future!
I use rattle cans and spray outdoors, too. I use a largish box as a spray booth and an old pillow case as flap that I lower to try and keep dust off. Works pretty good. Remember to vacuum it out before use!
Try wet sanding and reapplying the paint. Use very fine sand paper 2000 or 3000 grit.
Good Luck! and Welcome to the Forums.