Everyone's got great things to say about Jason/Fret Nation, and another option is John Fox (JFB). There are others too, especially outside the US.
The process with JFB was - pay a deposit ($1000 I think?) to get one of his build slots, already reserved. He sends a pricing sheet for all the options you have, you go back and forth with John hashing out what you want. He is the platinum standard for customer service and very knowledgeable! Then you wait an agonizing long time (but not as long as if you didn't have a build slot!) for Dingwall to be ready for your order. You don't have to actually finalize
anything, including the model even, until they're almost ready to start. Then you wait another agonizing long time, scouring Dingwall social media hourly for glimpses of your half-finished bass

and then... one fine day... they ship it to John, he checks it out, maybe takes some pics, and ships it to you.

Somewhere along the line, you also have to pay the remainder!
Disclaimer, my description's from my own experience two years ago. I've "only" done one custom, others here have a wider range of experience, including with Fret Nation.