I recall seeing a bass, or maybe it was one of those weird basses, the 6 string ultra-picollo basses, "guitars" I think they call them, that had pickups on sliding rails, so you could reposition them wherever you wanted. Atlansia makes basses with an array of pickups covering every spot and you can decide which pole pieces to activate for any imaginable configuration, but there's a reason Fender puts their Jazz bass pickups where they do, it sounds good.
I have heard that too many pickups create an electromagnetic pull on the strings, like a gravity field, that can interfere with the string's ability to resonate, that is to say, it can dampen their vibrations and interfere with sustain, probably more of a problem for thinner wimpy guitar strings, than for tough manly Bass strings, but I don't even know if that's true. Ace's center pickup houses a smoke machine, at least on some of his Les Pauls, you should put one of those in the bass you're making, that'd be cool!

(no, I'm not kidding.)
the first bass I built, 27 years ago, I could only afford one pickup and so I put it in the centre, probably I was imitating what I was basing it off of, my HondoII P bass, which had only one pickup. later when I realised the Jazz bass sound was what I really dug, and had a couple of EMGs put in, one in the centre, and one near the bridge, well it sounds very like a Jazz bass to me, tho the centre pickup seems a little closer to the bridge than I'd like, it's not that far off, in any case it sounds very nice. the bass I just finished building, I put 2 pickups in it, and tried to space them evenly. I didn't really put that much thought into it, I'm a little embarrassed to admit now! after I built it I looked at it and thought, hmm, I wonder if that isn't too much space between the pickups, even visually it seems like they're too far apart, though I wouldn't move the bridge one in either direction, but it sounds great, so there ya go. (
http://www.talkbass.com/forum/f57/bat-bass-749410/index4.html)
I started to look at that article linked to above in this thread and my head started to swim from all the science (and I used to fix TVs for a living, but that was 15 years ago), you're building this for your wife? take her to a store, have her try out every bass you can find and take notes about which ones she likes the sound of best. use that as your starting point, and for a long happy marriage, practice saying "yes dear". good luck!