If you need to make replacement windows here the the best procedure IMHO.

Make a paper template from the glass so that a correct cutout can be made.

Then you can place the plastic on the convex side of the glass if its not straight and place it in an oven and heat it so that the plastic deforms to the same profile.

There is a minimum temp at which plastics like acrylic or lexan will deform. I forget what they are but I am sure that the place you get your plastic can tell you.

Most plastic places can make the cutout for you if you don't have a band or skill saw, but I am not sure if most plastic places can do the melt for you.