I guess my problem is my lack of knowledge of how to describe what I want. To me the stock pickups sound a little thin(?). I guess I want something a little warmer or bassier (is that a word?). How would you describe the stock Geddy tone?
I find the Geddy to sound like a good 70's jazz bass. It has bottom end, but not the bottom I hear in my head. What it does not sound like is Geddy's, snarly, barky, low mid toned 72 jazz. They sound closer to his red jazz, but a little more open on the top end. After listening to, and reading a lot of info on pickups, my opinion is that this bass needs an overwound neck pickup. It is close, but not quite there. It only misses by a little though.
I play every Geddy that I come across in the stores to hear how they sound. Out of 9 basses only one had a dark, low mid bottom end. The rest sounded very similer to my current bass. A good top end, but diluted low mids from the neck pickup. Hence my opinion for an overwound neck position.
I can eq my bass and get closer to what I want, but the bottom tends to be a bit boomy as opposed to tight. Plus I lose the top end that I like in this bass.
I will probably go with a SD Ant. II, or a 2-3% overwound Fralins. The fralins Pickup appeals to me for it's tone, and I can get it custom wound. The soundclips of the SD pickups sound very nice as well. A set of Fender CS jazz bass pickups would work well also.
Search the board here, and look in the faq's section. There is a ton of info on J bass pickups.
Let me add as well. Setup on jazz basses is critical to unlock the voice. I have played with pickup heights extensively, to find the right balance. Be sure that you have explored your setup specs down to a gnats butt. Sometimes lowering your neck pickup by 1/64" can unlock a new voice.