The thing about 12-string guitars is they take 12 tuners and 12 bridge pins. Which is why I've hesitated on buying new tuners - with twice as many on the guitar, they cost twice as much.
I just reamed out the holes with my trusty bridge pin reamer. Five turns exactly got them sitting flush to the top of the bridge.
Then I used medium, fine, and swirl remover hand polishes to rub it out. I would have loved to use a machine on it, but I wanted to be gentle with the original finish.
I need to reglue the end so it's solid.
The Complete Martin Guitar Restoration Saga
Repairing heel break
DIY chisel for bridge plate removal
DIY bridge plate removal iron, Pt.1
DIY bridge plate removal iron, Pt.2
Steam removal of bridge plate
Bridge plate removed
Tongue brace removal
Crack repair and brace scallop
New bridge plate Pt. 1
New bridge plate Pt. 2
Patching hole in top
Final fitting of top patch
Installing carbon fiber rod
Fingerboard crack repair, Pt. 1
Fingerboard crack repair, Pt. 2
DIY fret bender tool
Refretting Pt. 1
Refretting Pt. 2
Tuner shaft repair
Neck reset - dovetail fitting
Measuring neck set with DIY jig
Gluing the neck with hide glue
Fitting bridge pins (This page)
Making bone saddle
Making a buffalo horn nut