I think there may be an interest here for people that would like to make replica overlays, overlays for games that could benefit from them but don't have them or homebrews.
I'll share with you my method for overlays. This is how I made the overlays for My Mario Bros. Controller set and a new one for Quest for Quintana Roo
1. Take your image with 9 overlays...then mirror it. (9 fit on 8 1/2" X 11" sheet)
2. Convert the file to a .pdf
3. take it to a print shop and have it printed on transparency film ( Office Max does it for about $2 a sheet)
4. take the transparency sheet (spray adhesive on printed side) and a sheet of regular printer paper and spray 3M Super 77 Multipurpose adhesive on both.
5. Let both cure for 30 seconds then flip the transparency over onto the paper
6. starting from one side use a craft roller to tightly bond the 2 pieces together and insure that there is no air bubbles.
7. Very carefully cut each out by hand with nice sharp scissors.
8. Slide into your controller and enjoy.
The paper backing makes it so that you don't see the keypad numbers thru the overlay.
This adhesive works fantastic and I spent a lot of money finding a good bonding agent. Not just any old glue will do.
Since the toner is on the backside of the transparency film and paper is protecting it, you don't have to worry about it scraping off.
If you wanted to get fancy you could get a Klic-N_Kut
and program it to cut them out. This cutter could also be used to cut out and score homebrew boxes.