Without seeing the crack I'll assume it's latitudinal versus longitudinal, which is the most common type of crack in a guitar neck.
I gather that the crack is at the headstock, hence the problems with the nut question. Is it at the scarf joint, if one exists, below or above it?
If I have it wrong, please correct me.
As far as the dowel pins, in order to do the dowel pins correctly you really need a fixture or jig to make certain the dowel pins don't throw the centerline off on the repair, and they're normally employed at the time if the repair, versus later. Not seeing the crack makes it tough to call, but if the crack is where I think it is, you'll need to drill in from the top of the headstock to get a good angle, then fill those holes later. I don't know what your headstock looks like, but unless you re-veneer the headstock the plug holes will be very visible...or you could just paint it.
As far as adding them after the fact, it probably isn't necessary. Since you've already glued it, they really are academic at this point. If you used a quality wood glue, like TiteBond, the glue joint is now stronger then the wood. A dowel pin isn't really necessary at that point, because if you don't have a good glue joint they could work against you in the long run. And you definitely don't want to interfere with the truss rod by either nicking it with the drill or wind up gluing the truss rod into it's channel inadvertently.
Normally, a broken headstock, that broke clean, is easier to repair then a crack because you can achieve a better glue bond surface. The hardest part of repairing a crack is being certain the wood is clean when you make the glue bond. Any dirt, oils or polish in that crack will raise Hell with the adhesion.
This is a bit after the fact, but standard TiteBond glues can be thinned with up to 5% water to allow it to flow into the crack better. Hide glues can be heated to achieve the same purpose, as can polyurethane glues. I would use a thinned glue and a disposable hypodermic needle to shoot the glue into the crack. It does make a bigger mess to clean up later, but at least you can be certain that you've penetrated the crack as far a possible with the glue.
How did you clamp this repair?
As far as repairing the nut shelf, the only wood filler I ever use is epoxy wood filler. It's strong, sands flat and never pops out if your surface is clean. Granted, it's a pain to sand, but it accepts glue as well as the wood for the most part.
You might want to pick up a nut seating file for this job. They look like this:
Use the epoxy wood filler sparingly, and scrape away as much excess as you can before it sets up. Give the filler 2-3 days to set up and file it flat for the nut shelf.
And I'd let that repair sit for at least 3-5 days before I put any strings back on it. Don't bother to refinish it until you can test it first. And listen for cracking or creaking while you tension up the strings. Let it sit overnight and check again to see if the repair held. If it makes it overnight then pull the strings and refinish accordingly.
One last question. Is the fingerboard effected by this crack at all?
12 strings can be problematic, depending on how they were originally constructed. Any dings or drops can become instantly severe on 12 strings as well. They sound great, but they really need to be babied.
Keep us posted on how this one holds. And don't feel it's the end of the world if it breaks through completely. You can actually achieve a better repair on this neck if it does.
Happy Trails
Cynical One
