I can immediately think of two perfectly good ways to perforate film. The first would be a matching set of male and female rotating dies which pull the blank film in and push it out with holes in it. The other way would be a flat male and female die which cuts a small lengh of the film which is then indexed along and uses the last two perforations cut to register the next set.
The rotating dies method is the way to go if you are doing a lot of film and want to run fast. The flat die method would be easier for a hand operated, low quantity production run. We have small hand operated machines at work similar to this for punching polyester sheet.
If you were happy with round perforations, a pair of drilling heads and an automatic advance mechanism would work but I would rather deal with perforation sized pieces than the swarf from drilling.
What we need to do is scale it up. Make film just over four inches wide and perforate it with larger holes to make easily advanced rolls of film for large format cameras!