I can't open your file, but this is what I did.
I created my artwork with a crosshair centered in each hole for buttons, joysticks, etc.
Then I placed the artwork on my CP board and center punched each cross hair.
I then drilled out the CP where the punch marks were.
The lexan CP cover was then placed over the CP board and routed out.
The artwork was then sandwiched between the lexan and CP board.
I cut out the artwork with a razor blade.
Good luck!