I've done custom orders/builds twice now and my advice is this:
Try out an example of the luthiers' work first. Even if it means organizing a meet up with someone who has an example of their work - a Bassbash for example would be perfect for this,
Make sure you know EXACTLY what you want, down to the last screw. If there's any doubt or you have no idea about some part of it you are possibly leaving yourself open to an expensive disappointment,
Is there a current manufacturer of something similar to what you want? Why not see if they'll do you a custom version to your taste,
What about a Warmoth/USA Custom Guitars home build?,
If you want to protect your investment then why not find a vintage bass rather than a custom build and see how you get on?.
As said before take your time and look at it as a long term research & development project and enjoy it!
Regards,
Jon