It is a good to glue the dowel stick to the neck before doing the fret work. After the frets are on the surface of the fingerboard will no longer be flat, making it more difficult to clamp the neck to a jig for possible modifications.
Joining the dowel stick to the neck can be a tricky maneuver and takes place after the rim has been turned on the lathe and the rim dowel stick hole has been cut. It is essential to check the fit of the dowel stick in the neck and the rim. The dowel stick should fit snugly through the rim dowel stick hole with the rectangular portion of the dowel bearing against the sides of the hole. The tenon portion of the dowel should stick out of the rim about 1.5″ or a little more. It is important that the rectangular portion of the dowel terminate just below the rim’s outer surface. It may be necessary to trim away at the outer corners of this rectangular portion of the dowel with a file or a pocket knife. If the tail end of the dowel is too long it will have to be trimmed. You can come very close to finding the correct length of the dowel by inserting it in the rim and measuring the rectangular portion of the dowel that protrudes from the rim dowel stick hole and subtracting a little less than that amount from the total length. The flat end, or tail of the dowel that bears against the inside of the rim will need to be rounded to match the curvature of the interior of the rim.
When you have the length of the dowel just right, insert it into the rim and use a screw to secure it in place. Take a look to see if the stick looks centered. Then, set the neck on it and see how it all looks. Does the neck fit snugly against the rim? If not, what is holding it out? Does the dowel stick look straight with the neck? Trim and adjust the dowel stick as necessary. If the dowel looks a little crooked in there it may be remedied with a few licks on the jointer. Be sure to remove wood from the side of the dowel that looks heavy. I leave the portion nearest the neck at the full dimension of 1″ x 3/4″. I often taper the stick below that on all four sides, but just as often I leave the stick rectangular for its full length. Only a little taper is needed to correct any problems with visual symmetry. Be careful not to taper the stick too much.
If you have found that there is some issue with the radius or angle on the heel of the neck consider it very carefully. In this case it can be helpful to apply a thick layer of chalk to the area of the rim where the heel of the neck bears against it. Set the neck back on the dowel after the chalk has been applied; the chalk will rub off on the areas of the heel that contact the rim. If the fit is good, chalk should rub off on the mating surface of the neck heel uniformly. If chalk is only present here and there on the mating surface of the neck heel that indicates that more trimming is required. These are the high spots and will have to be trimmed away with a file or pocket knife. After trimming check and trim and recheck until the chalk rubs off uniformly onto the mating surface of the neck heel radius. If the neck is still not fitting perfectly, it could be that the radius is too large or too small. If you have plenty of neck heel material, the radius may be re-cut or re-sanded to make the fit better. If you find that the radius of the heel is off, it is wise to check that your jig has the correct radius and that the rim has the correct radius. Experiment with scrap material until you are sure the jig will deliver the correct cut.
After you have made a perfect fit between the heel of the neck and the rim it is time to join the neck to the dowel stick. Epoxy is my choice for glue in this operation. Finding a good way to hold the neck in place while the epoxy sets can be a challenge. Long bar clamps may be used. A long, stretchy piece of an inner tube might work as well. Mac makes his dowel stick to fit pretty snug in the neck heel dowel stick hole, so snug that it is difficult for the excess epoxy to squeeze out. So, he drills a relief hole in the heel of the neck to let out the excess epoxy. After the stick and neck are joined he puts on the heel cap.
Leave the dowel stick screwed into the rim. Figure out the fit and clamping procedure without the epoxy, that is to say, do a dry run. Before mixing the epoxy get some wax paper and cut a piece about as wide as the rim is deep and 5″ or 6″ long. Cut a round hole in it that will allow the round end of the dowel stick to fit through it. This will keep any excess epoxy that might squeeze out from bonding the neck to the rim.
Go ahead and mix the epoxy. Put some inside the neck heel dowel stick hole and put some on the tenon end of the dowel stick. Fit the neck down onto the stick and wipe away any extra epoxy that squeezes out. Fit it on and clamp it down in whatever way you’ve found that works. Make sure it is not tilted forward or backward, or rotated in any way. Look at the place where the heel of the neck meets the rim, is it evenly snug? Is the backside of the heel sitting snug? Make sure it is all snug and then let it sit while the epoxy hardens. I usually give it 20 minutes and then take it apart, if you wait too long it may be difficult to remove the neck and dowel stick from the rim as they could become trapped by epoxy squeeze-out on the inside of the rim.