You get a great improvement in the tone of the Epi EB-3 mudbucker if you do one of two very easy and inexpensive things:
1. Take the two pickup coils out of series and wire them in parallel. They are wound to such a high DC resistance when stock. I think mine was something dumb like 30K or more! This kills definition and makes the tone harder to tweak, because you're starting point is a high output, treble-attenuated tone. Putting the coils in parallel really tames the pickup so it becomes something that can be tweaked a lot better with e.q. and gain. It gives you a clean, low output starting point, with which you can do practically anything in terms of tone shaping. It also makes it possible to truly balance the output levels of the two pickups, which makes the bridge pickup more usable in the real world.
I would also pad the pickup with tape or foam while you are in there. It sits loose in the pickup rout, held in only by the pickup cover. The pickup being held in in this janky way can cause annoying rattles.
2. Replace the pickup selector switch with a passive bass cut control (like G&L and Reverend use). You'll have to experiment with pot and cap values, and ideally you want a reverse audio taper pot. But it's not hard to do, and it's very rewarding tonally, especially with that bass.
I didn't ever replace the pickup cover on mine, but I wouldn't be surprised if doing so opened up a bit of top end clarity as well. The Epi covers have traditionally been quite bad in that regard (not sure if they have improved since I formed that conclusion, though...or if anyone else makes covers that are any better, for that matter).
The standard Seymour Duncan mini humbucker pickups (available in three outputs) are good economical replacements for the bridge pickup. They're built basically like old Firebird pickups (i.e. with blades, not a pole piece per string), so they work quite well for bass.