I have yet to "nail down" who is making necks for the custom builders. Most admit to using Warmoth at least some of the time. Almost anybody can bolt together a Warmoth bass. To Me the neck is 90% of the perfect bass. Sure there are a ton of Electronics to chose from. Alder or Ash??? Nitro or Poly??? Just think of the incredible bass you could build yourself with $5 Grand. I don't think you could even get it 1/2 that high. I have a custom builder that will sell me one of their necks but they won't give up the Manufacturers name. So it could be Mighty Mite for all I know.
Of course there are plenty of builders that make their necks from scratch. I know mine does.