Definitely a Prima Artist 6 string, because even though I like the colors of a Z, this is going to be [u:2kcrzwyb]the be-all, end-all of basses[/u:2kcrzwyb].
ELECTRONICS:
I too was just thinking yesterday about a Z3. I would want mine to have a three-way toggle to select which pair of pickup signals to send to the rotary switch. I think I'd have Sheldon install an FD-3.4 in the neck, my extra FD-1 in the middle (bridge 1?), and a Mach II in the bridge.
-In addition, I'd go for a Piezo with a blend knob after the rotary switch.
-I'd like the 13-pin output jack, so it's ready to rock without a MIDI pickup.
-Preamp: OBP-3, 18V of course.
-Also bluEQube, because it CAN be useful, though I rarely have it in.
-Hybrid treble.
-I'd prefer an active/passive switch, rather than the push/pull, because it just seems nicer to me.
WOODS:
I LOVE the way the Prima Artist in the Bass Player Magazine review looks. To that end, I'd like mine to look similar.
-Sheldon's choice of body woods. I don't care what they look like because they'll be well-hidden, if you know what I mean.

-The only part of the body wood visible on the face is that Walnut bass-side. Because of that, I want a light contrasting light layer, and a dark top.
-Contrasting layers of AAAAA Flame Maple, top and back.
-A dark, heavily figured top and back wood. I think that the BPM reviewer had Wenge, but not sure. Whatever it was, it looked awesome. Note: I dislike Cocobolo, because it matches a lot of furniture in my house. I'm buying a bass, not a table.
-Matching headstock, pickup covers, knobs, control cavity cover, and battery compartment cover. I'm sure the FD-1 and Mach-II would need to be modified, but if I'm paying this much, I wouldn't mind paying a little more.
Neck:
-Woods are definitely Sheldon's choice. He knows a hell of a lot more than I do, and I want a ridiculously firm neck.
-Neck finish: Oil/Wax. I love that smooth feel.
-Definitely want graphite reinforcement. Living in constant humidity changes, it's a must.
-As I've seen on some basses with wide necks (read: 6 or more strings), dual truss rods. I don't think Sheldon has ever done this, but I'd like him to try.
Fretboard/Markers:
-Ziracote Fingerboard
-Mando Frets
-LED side dots would be cool, but certainly not a must. If not LED, anything easily visible would do, but probably abalone to match the face markers.
-Face Markers: Abalone. Bars under the E-string frets 3, 5, 7, 9. "D" logo inlayed at 12th fret. Bars under G-string frets 15, 17, 19, 21, 24. (I find this more functional, because with 6 strings, no face markers, and slanted frets, it's easy to lose my place up high on my ABII.)
MISC.:
-Also, if you look closely at the next-to-bottom picture on the Prima Artist gallery page, you will notice not one, but TWO D-tuners. That's what I want, and I'm considering it for my ABII already. I have noted to myself that this would only work on a 6-string because of the tuner spacing.
-Definitely 24 frets. I don't know why it is, but I just like the look of 24 frets more. It seems more "complete" to me.
As you can tell, I spend WAY to much time here.