I don't think it is acceptable for a guitar maker to excuse body damage, untidy work and bad electronics by saying that the instrument is 'a prototype'. That's garbage. You asked for a neat, clean and functional custom instrument and have paid through the nose for it.
Reading through the topic, I see he's going to do remedial work so you are satisfied with it.
That leaves you without the bass for a period, worried about how it will turn up next time and hopefully not out of pocket.
All for the stuff he should have got right as a matter of course.
I really do hope you get your dream bass back and would love to see full photos (logo obscured if need be). I totally understand not naming the builder while you are dealing with getting the faults corrected.