There is no need to add a physical object to the screen assembly. Also, shooting through clear photographic film will probably not be satisfactory...because it's not actually very clear at all, depending on the film used. Graphics products might actually be clearer, but carry the same annoyance of statically-attracted dust.
I suggest you inscribe the necessary lines on the screen using a fine pointed pencil or very fine point marker(extra fine Sharpie in the USA). Pick any color you want!
If you really need to erase all traces of the inscribed lines later, a washable water-based marker might clean up more easily than the "permanent" Sharpie ink.
In the past I did it with a Sharpie and was able to wash off the marks later using methanol. Of course, handling the focusing screen this much invites permanent scratches and marks.
Measurement and marking will have to be very precise if you want exact agreement with the framing of the shots on film.
I advise using a separate 'junk' screen so you can skip the delicate cleaning after use.