I am doing the same thing myself right now if there is anything left of the old ones just make a template out of rice paper and do the side that needs replacing.
I dont have the old window layout any more,mine went with a crash years ago so I just went to towerhobbies and made a paper template that is close to the stock one.
just tape the paper to the plane and draw the windows in on one side,then cut the template out and just flip it for each side so its symetrical of course checking for fit.
I am using black adhesive backed covering instead of monocoat it works pretty good.