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Dip a dowel in wood glue—I recommend Titebond II—and press it into the screw hole in the neck. Using a small hammer, tap the dowel down to make sure it penetrates the full depth of the hole (Photo 6). Repeat this process with the other dowel.
To ensure a solid bond, it’s a good idea to let the glue dry for several hours or even overnight. When the glue is completely dry, cut the dowel flush to the heel using a small, flexible saw.
Marking the dowel. With the neck dowels installed, glued, and trimmed flush to the heel, set the neck back in the pocket and install the third neck screw (this is the one that screws into the metal insert mounted in the neck). Tighten the screw just enough to seat it against the neck plate—don’t torque it down yet.
Gently clamp the neck onto the body and add a little tension again to the two E strings. With the neck pivoting on the third screw, shift the neck from the bass to the treble side until the strings are properly aligned. When there’s an equal distance from the outside of each E string to the edge of the fretboard, stop and tighten the clamp.
Being careful to preserve your alignment, flip the guitar over. Insert the two upper neck screws into the body and gently tap them with a small hammer (Photo 7). The resulting indentations will mark the exact location for the new holes in the neck heel. Now you’re ready to re-drill those holes for the neck screws.
Drilling the new holes. Remove the clamp and neck from the body. Mark a 1/8" drill bit to the proper depth (you can use the 3/16" bit as a reference, or repeat the measuring process you used previously). By the way: The neck screws are 5/32" in diameter, so by using a 1/8" (4/32") drill bit, you’ll be sure the neck screw threads will “tap” the neck enough to hold it tight.
Double-check your drill bit depth: If you don’t drill deep enough you can crack the heel when you bolt on the neck. And I don’t have to remind you what would happen if you drill too deep, right?
Now, using the indentations you made as guides, drill new screw holes in the dowels (Photo 8). Again, using a drill press is ideal.
Install the neck screws. With the new holes drilled to the proper depth and diameter, install the neck screws. Check your work to see if the two E strings line up correctly with the fretboard edges (Photo 9). If so, congratulations—you’re now ready to string up your guitar and give it a workout.