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As noted in my construction blog, I made some Delrin pins to fill the tuner shaft holes to keep the finish out of them. (Teflon would probably be better, but I don't have any.)

Does that seem like a good idea? Is it even necessary? What do other people do?

I either use a reamer to clean them out afterwards or run a drill bit through them. The biggest issue I have had is with an epoxy pore fill.

I drill mine after the finish is applied and leveled.