which reminds me, were the cutout dimensions to the outside or the inside of the cutout?
The dimensions were of the actual art inside the hole, or as you put it, the inside edge of the cut-outs. Probably the best way to do it would be to produce the art to the exact size it's supposed to be. Lay (don't stick) it on the outer piece of the canopy (with it clamped to the middle piece to make sure the alignment and placing are accurate, and trace the shape of the art onto the outer piece. Then unclamp and cut the shapes out of the outer piece. Verify the size is a very close fit (perhaps a tiny bit small and trim the art to fit). Then just route a beveled edge - angled out - around the holes. Paint all three side pieces black. Route t-molding grooves in them and install t-molding. Clamp them together in perfect alignment and drill holes for mounting screws from the inside (probably 2" screws) all around to make sure they stay together nice and tight. Figure out how to mount it to the rest of the cab.
Since it was almost impossible to remove the canopy without damaging the rest of the cab (due to stresses from internal nailing), it would probably be a good idea to take some design liberties and figure out a way to atttach the canopy so that it can be removed easily, while maintaining the illusion that it is just as solidly attached as the original. It might also be beneficial for moving if the same was done to make the seat assembly detachable as well, especially since it appears that way from outside. Actually have to look at the bottom to see that it is all one piece...
As for lying the cab on it's side for exact measurements, it's easier said than done, especially with a game worth a couple grand that doesn't belong to me. And some minor (and major in one spot) corner damage would still throw off an "exact" tracing, even if my hand was steady enough when cutting to get good results anyway. (I can just see trying to get underneath the feet area to trace the side covered up by it.)