Well, Paul,
as per your request I tried figuring out a ballpark list price for this bass, but it's hard, you 've got so many unusual features...only Mica or Susan can answer those with any authority. Having said that, there are a few things that can be figured out.
For a custom neck-though bass, as I've said elsewhere, I think the Rogue model makes an excellent starting point, and it also comes standard with the 35 inch scale you desire. That would start you at 4300$.
Now for the Body: The Excel as you know is a set neck bass normally. Obviously Alembic can make a neck-though version; however, unless I'm much mistaken, this will cost extra money . The Excel , like the Orion has those wide cutaways that make it harder to carve the heel of a neck-through... If I remember correctly, to have one of those shapes made with a neck-through is an extra 150$, but of course Mica is the ultimate authority on this.
The Macassar ebony top is 900$. The bookmatch to center is currently an extra 350$.
The Neck: an 11 piece neck with 5 ebony lams is gonna be really pricey I bet...a 5 piece with 2 ebony lams is 1450$, so my guess would be a cost about 3000$ extra or more ( hope you've got a good chiropractor there, Paul, this baby will weigh a ton).
The Peghead: I'm a little confused by your description of the logo, it sounds like you want something similar to the shell logo, but in brass rather than silver ( which is a 750$ option), and I have no idea how much Alembic would charge for that, but it'd probably be something along those lines.
The fretboard: Fretless is no charge, but I believe sidelines position markers( the teeth ) are an extra 150-200$.
The Electronics: here I've absolutely no clue. I think it will all depend on how much work Ron would have to do. If he has to come up with new wiring it might cost you as much as a regular set ( 2 pickups) of series electronics; but then it might also be somewhat cheaper; once again, Mica can tell you. I also would think that the XLR jack would not give you a stereo sound, but maybe a balanced signal, and I guess you still would need it to power the bass through a DS5.
Of course, I'm sure you're aware that in the future things might change ( woods get more expensive, costs in general go up ) and this will cost even more, but it seems to me that right now you are looking at a list price of 11 to 12 thousand maybe even a little more.
Well, this is it brother Paul,
I had fun researching your bass, I hope you find this helpful
Good luck
Valentino