First, some information:
Bubinga, Ebony, Afzalia, Cocobolo, Ovangkol, Wenge, Rosewood; these are some more dense woods that project a lot of tight, focused, high mids; the "sharper" sounding woods. Warwick has made a reputation by including these woods somewhere in the construction of most of their basses. Cherry is another somewhat dense wood, and used to appear more in Warwicks.
Maple and Walnut are pretty balanced woods... they put out a fairly even range of sound (consider the popularity of maple).
Swamp Ash, Poplar, and Alder are probably the most common of the not-so-dense woods; these woods are more porous; they trap low-end and low-mid frequencies, and they have more of a "boom" or "rumble" to them. They sound "fat", and don't have a lot of definition.
Consider this: the Thumb BO has the following specs:
Body: Ovangkol
Neck: Ovangkol
Fingerboard: Wenge
you know what it sounds like.
The 2006 Limited Edition "Dirty Blonde" Thumb BO has THESE specs:
Body: Swamp Ash with a Poplar top
Neck: Maple
Fingerboard: Ebony
I can't think of two basses that sound more different. Speaking just from the perspective of the woods, the Thumb is engineered to project a ton of midrange, while the woods for the Dirty Blonde have been selected to naturally SCOOP most of the midrange out; the Ash/Poplar combo provides big, fat, boomy low end, while the maple/ebony neck adds some top-end snap. It's a very "clean"sounding bass, with almost NONE of (oh, I'm going to say it...) "that Warwick Growl". I call the Dirty Blonde the "Warwick for people who hate Warwicks".
Anyway, when selecting woods for your bass, you want to pick woods that COMPLIMENT each other sonically, then consider factors like looks, weight, and cost.
Now, on a more personal note, Mike... I've gone back through our correspondence, and nowhere in any of it did you mention your preferred choices for woods. All we talked about were twin J pickups and piezo pickups. I'm sorry if you feel slighted, but I really was trying to help you out to the best of my ability. If you'd asked about woods, I'd have been happy to put in my two cents about that as well.
The custom shop isn't making decisions on a whim, and neither are Ollie and I; there's just a lot to consider.