The Bart Mk2's in your bass aren't really a standard size, unfortunately. You'll need to do some routing to get new pickups to fit.
For me, I'd consider ordering pickups in the G6 size. You'll need to do a bunch of routing, but, since these will be bigger than your existing pickups in all dimensions, you won't be left with gaps between the new pickups and the existing routs.
Another option would be to order some pickups without covers, and get them put into wood shells that'd fit the rout.
Anyway, pickups I've used that I'd recommend:
1) Nordstrand DC (parallel) - there are two winds for these dual coils; I'm currently using the parallel wind for jazz fusion and I love 'em (you can get the series wind if you want a darker, louder pickup - I've heard them used for fingerstyle rock and they kill). The parallel DC's sound similar to Barts with a more open top end, and a more upper-mid content. Great for slap as well.
2) Bart Classic Bass - they're Barts with a brighter top. Big, full, darkish compared to the Nordstrands but not as dark as the non-CB Barts.
One thing I'd recommend is looking at swapping the preamp instead. The frequency centre of the BTB preamp's Bass control is way too low (I recall it being like 20Hz or something silly like that). Boosting bass will devour headroom and made you sound super boomy. If you want a darkish preamp, but with better EQ points, the Aguilar OBP-3 gets great reviews.
I'm currently using a Mike Pope preamp (4 band) which is sort of stupid awesome. Very tweakable and useable. Only thing I'd say is that it doesn't play well with my GK rig for some reason (it's pretty hissy with the GK), but works swimmingly with everything else.
Also, welcome to modding. It's an addiction. You're never escape, never!