I think you've answered your own question. You are a craftsman.
I visited the website the other day, and it's pretty neat. Not many hand built pickups out there any more. That in itself makes for some interesting problems I'm sure. Most musicians know EXACTLY what they want, but they want it now. They can also tell you scales, and modes inside and out, but can't remember what they had for lunch.
Seems like you need to get a system in place to track these orders to keep your sanity, and your customers.
Most consumers think that they are the most important thing in their world, and yours, and want to be treated as such.
As Shuie says, I'm sure you are a fist class guy to deal with, but the ordering instructions you posted tend to plant the seeds of doubt to someone that doesn't know you from the Pelican board, or a repeat customer.
As far as the amp builder, his policy would ensure that he would never get a penny of my money, no matter how good his amps are.
Good luck figuring out how to handle the problem, and I'll keep checking your website for the P&J- Bass pickups.
I've got an older practice bass with EMG selects, and it just sounds a little off through the Bassman 10.