I walked into his shop this morning and he was finishing up taking in a repair order from someone. I stood silently and politely with my bass in the gig bag until he finished. The other customer left and as soon as he looked up and noticed me he said, "I was just writing you back. Listen, I will do my best to get you a Fender body. I will do right by you. I will make sure it is already pre-routed." He said he used a template and then something something something. He was very apologetic. I offered to show him the bass to which he said, "no I don't need to see it." Which means he knew he did it. I told him I called Fender and they can't help us and that they said to use Warmoth. He agreed and said he'd order it up today. I told him about the LPB that was there yesterday (according to another poster here) and he asked, "but is it routed for the jazz pickup?" I said no and he said "I'll have them do it." He said he would do it free of charge and apologized profusely. When I got home I went to the Warmoth site to see if that body was still there and it's not, so I am hoping he already placed the order as soon as I left.
Long and the short is, he admitted to his mistake and is willing to fix it free of charge. This made negotiating a lot easier.

I'll keep you all updated.
This story may have a happy ending!