Kevin,
To my knowledge, my JAE Spyder will be the first replica ever made with Series electronics. In fact, it will be the first replica ever made period! It will be different in the sense that it won't have the Series I and a half electronics John had - he had Series I electronics with two master volumes on the lower horn and a switch to choose between each. Mine will have the two master volumes as well, but with Series II electronics instead. It will also not have the flat radius John had on his fingerboards (after discussing this with Ollie, I learned that this was personal preference on John's part - I like a radius myself). I plan also to have the neck thinner at the nut - I sometimes have difficulty reaching the F on the E string in first position due to the width at the nut on my Spyder. And of course, it will have the note inlays John's basses were famous for, as well as the other stuff (e.g., bird's eye maple, spider webs, etc.). I also plan to move the neck pickup back a bit - very difficult to slap or pop it where it is on my Spyder. Finally, the body will be like John's Spyders, which are different from the limited edition run. Alembic made the bodies a bit different from John's so as to make them more appealing to a wider audience.
So it won't be an exact replica, but pretty darn close.
And yes, it ain't cheap!
Alan