Yes, that's a good idea and, as you say, it'd look as though the stickers are affixed to the window. As you only get one shot at it, you have to be sure it works. What I did with the tax disc circles was to cut out a bit of cardboard that was heavier than any of the Emission stickers and had that on the windscreen for a few days.
The clear self cling material you suggest should work as it is probably lighter than acetate and will have a full surface area to cling by..
Randa