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I'm also not convinced that trying to line up your plate with a printed template and line up a powerful enough light with each hole to get a clear point projected on the template in the right place is going to be any easier than just doing as Loyce has suggested.
As I have mentioned in my first message one can project light that has passed trough holes on CCD matrix, then assign coordinates of that matrix to a letters that correspond to the certain holes . This way you eliminate the need to use a printed template.
And don't worry about the luminous intensity needed for this. The plates with drilled holes are used to map the long-distance galaxies of Universe by exactly the same technique I have suggested.