Tuning Advice needed: removing burrs from barrel set screw holes?

Gota couple options. From the sound of it, you cant get to it with a dremel bit (I ususally use round diamond bur bits for this). If that's the case, you could use sandpaper. I'd probably tape some to a dowel, and go at it from an angle, just using the tip of the dowel and some pretty fine paper. Go slow, and keep checking your work and placement.
 
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I’m not familiar with that exact model but the raised burr is in a soft metal, either steel or bras maybe even stainless steel. In any case a manicure nail board like in photo should do fine. If you’re trying to avoid removing bluing or black oxide just do it very judiciously.
Anytime I designed and built something that assembled like that I milled flats on the shaft (OD) portion so burrs would not raise above the diameter.

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I like to use flex hones sold in different diameter and grit. I am usually just cleaning up airtubes after reworking or during resto work. If you just want to go cheap, get a dowel you can chuck into a drill. Build up a few portions with masking tape to fit the hole, undersizing an area to be under the offending screw holes. Wrap the undersized areas with sand paper. Insert to line up the sand paper with the set screw hole and mark the dowel as a reference on depth. Chuck it up and clean up the area. Then back it out spinning to prevent gouges. You may need to repeat with finer grit to get any scratches out.