[AZKen]

If you wish to abandon the template:

Use a laser level to shine on the hole(s) with panel off. Don't move laser or door. Install panel and drill or mark on the laser X/Y center. A mechanical way would be to take door off, lay it flat and use a plumb bob like the laser method.

BUT, not sure exactly what you are doing. Did you make some custom door panels?... and need to make window crank and door handle holes.......or are you talking adding arm rests??????????????????