One thing you might want to do is find out precisely what Squire did to his basses, besides removing some wood.
What did he play through?
Did he change the tone circuit? A lot of people did in Ric basses, looking for a way to get their low notes back (low E has a tendency to disappear).

My guess is that it will have a bigger effect on the sound.

-A

I think he used Marshall guitar amps/4x12s back in the day. The reason I was specifically interested in the pickups is because I believe he only used the neck pickup, so it seems like in his case it would make quite a bit of difference. I'm not too bothered about it sounding exactly the same (it'll be used with a YBA-1A and either a 2x12 or 1x15 anyway), I'm just interested in getting more in that area than the standard 4003 sound.

More like the sounds on Close to the Edge or Fish Out of Water, actually. I'm well aware that 95% of the tone is in the playing, I just favour that sound, and I like the way it looks, so why not? As I've already said I'm not wanting it to sound exactly the same, but in that general ballpark, which the stock 4003 doesn't quite get, to my ears.