I looked at ours (see the photo I uploaded) and the top of the plexiglass slides into a slot at the top of the window opening that is then caulked. I think it's the same thickness as the one that opens, but to be sure measure the port side window thickness then see if it will slide into the recess at the top of the stbd window opening.
Your idea of making a template makes sense, but you should make it out of something rigid, like thin plywood. You could also get the reinforced plastic for patterns (like Sailrite sells) and tape it over the opening and trace where you want the edges of the plexiglass. You might want to go a tad oversize since you can sand it down easily but when it's too small, it's all over.
I didn't see any special shaped cutouts on mine, it was pretty plain. Measurements would be tough since it isn't regular, but if I can provide any other information let me know.