I'm not sure where the joke notes were, but I was asked about this and decided against having them put in. As I saw it, there was no way I'd ever be able to have an exact replica made - all of John's Exploiters, to my knowledge anyway are in private hands now. I'd have to have one to make an exact copy, and that simply isn't possible. What I set out to do was get very close, and make it more playable for me. After all, I'm the one playing it, not John or anyone else.
All this being said, I felt that not having a joke note was a tribute to the man - he was one of a kind. So were his basses, and I felt that it should be left that way, joke notes and all.
In the end I think Alembic has created a very close replica for me, with certain changes. During the design and construction, Susan and Mica both told me that certain things may have been mistakes on the originals, e.g., placement of the controls near the bridge, etc. As I felt John would have opted to fix these things had he ordered another Exploiter, I went ahead and made those changes I thought necessary from both an aesthetic and playability point of view. The end result, I'm sure, will be the bass of my dreams.
Alan