Lots of purchased items come in transparent molded plastic. it's stiff, almost 1/128th". Just cut a flat piece to size, and glue it in.
MonoKote is allowed, but better off with EconoKote that comes in strips and sticks once rear coating is removed.. But I wouldn't like it for side windows.
In looking at the last of your pictures, showing the bottom. As a quick ability to remove body from chassis. Shape and glue in the two side pieces. In each side piece, drill two concave indentations about 1/4 inch deep. Then on the chassis, insert a round 1/4" dowel, with rounded edges at each end. The dowel should stick out of the chassis about 1/4 inch, so they can fall into the concave indentations. The plastic bodies flex enough so that you can pull the sides apart a bit, and snap the body to the chassis.
If you measure your indentations and dowels exactly, you could really quickly change bodies if you find one that has better aerodynamics.
On both bodies and Chassis, remove as much weight as possible, allowing more weight to go to the rear. But you have to be careful on some setups where the body has a long rear behind the rear axles, that you don't put in weight such that the car does a "wheelie" at the tracks transition point.