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Where do you put that line?

I would get it adjusted before I drill the holes. Then if you have to move it a very slight amount, you will still be able to move it due to the difference between the hole diameter and the bolt.

Clamp the mount where you want it and use a small bit maybe a 1/8" and drill through the mount and what it is going on. Do all four holes. Then drill the mount out to the size of the bolt and what...

I can't picture what you are asking. Are you going to tap it and bolt it from the back, drill all the way through and use a bolt and nut or is there a flange?

What kind of breakout board do you have? Is it home made? Can you post a model number or some pictures. I'm sure we can figure this out. Just post as much information as you can.