you could still put in your custom inlays.. a-matter-of-fact i think carvin (which is a Christian based company) will install them for you, my only gripe is... its still a carvin neck

.. not your design, let alone a design custom made for your feel/hands.. how often do you find yourself freting the body?
If you were to design your own neck i think coring for the truss rod would be your biggest challenge.. If it were me, (maybe someday it will be).. id find a local luthier, get buddy-buddy and throw him a few bones to do some of the stuff that would be out of reach, both financially and skillfully. (like buying a drill press or whatever that can core the neck 35" plus... the rest i think is pretty straight forward..
its just a matter of choosing the right glues for resonance etc, all the little things matter !! as much as the woods... id for sure go with brass nut hands down.. first bass id keep electronics simple and do bartaloni precision/jazz active pickups.. or emgs whatever.. obviously price will be an issue.. remember when it comes to sound, the finish also plays a role in this thing.
again the truss rod is where id have a prob, cuz i cant think of a correct way to do it at home without the cost of major machinery.. this is the key, you bore it with the slightest bow and your in buzz city..
btw, i happen to like carvin great stores/people.. when i bought the equipment for the church in california we went carvin... outstanding quality for the buck..
peace,
rob