Where to start? Lots of good comments while I've been sleeping!
Those Sperzel tuners look nice and compact. I will certainly consider them for my next project. I got my set of Gotoh tuners for $25 delivered, so they were a bargain. I'm assuming the locking mechanism keeps the instrument in tune better(?).
This is a complicated build for sure....a lot (all?) of it is because of the headless, twisted neck design....but that is also what makes it worth doing. If I wanted a traditional bass, I would have bought one for a few hundred $$$ and been done with it.
I would consider making neck blanks, but then everyone will want something different (# of strings, width, length, fret placement, etc..). I can see it snowballing and I haven't even made one yet!

Let's see how it goes....
I like the pic of the cat! It cracks me up.
I originally was going to use ferrules and string through the headstock. I even ordered the ferrules. I realized after looking at them and the strings that the strings would need to make a very small radius turn to lay flat on the zero fret. This turn would be over the sharp metal edge of the ferrule with the thickest part of the string. The string is doubled up around the ball and the headstock is only about 5/8" thick or so.
I checked and a 4-40 bolt is basically the same size as an M3. I have 4-40 hardware in my shop so I can mount up a string between a tuner and a 4-40 bolt. I can empirically test the setup. I am not worried about ruining threads because I will never need to tighten or loosen the bolt while the string is under tension. I did some quick bending load calculations, and the bolts should be able to hold the tension of tuning, but not sure about playing! Plus some of the measurements/calculations were estimates and assumptions.
Dowel pins would be a lot stronger. I guess if they are angled away from the tuners, they should keep the strings on just fine. I don't want the balls moving around on the pins as that will mess with the action.
The pre-amp that I was going to get at GFS went out of stock before I could buy it, so I'll just be using a blend pot until then. That should make the electronics a snap. I'm pretty much ready to go except for that. Hopefully I'll start cutting something in the near future.