From what I understand the only drop-in pickups are made by "Hippo." I know the stock pickups get slagged quite a bit, and maybe I'm just lucky, but I'm perfectly satisfied with them. Of course they're not Bart's or EMG's, but the instant I changed out the stock strings I decided to keep the pickups. I used DR Fat-Beams, which are pretty high-mass and the output increased dramatically - at least 5db. After that I stripped it down and did a full setup: full level & crown, shimmed the neck (angle was too shallow), filed, cleaned up, and shimmed the nut, then balanced the pickups. The action is super-low (I don't have a ruler precise enough to give you an exact measurement, sorry.) and the sound is well balanced and bright, from the low B all the way to the highest frets. Chords ring out nice and clear, and it can get nice and aggressive when need be, which is a nice benefit of the 34" scale (35" B's sound too stiff to my ears - I like a little slop without drop-tuning.) But overall I play with a fairly light touch, and it responded quite nicely.
Trying for a more vintage tone, I slapped on some Chromes I had left over from another project. Terrible decision. The C string sounded choked, and the playability suffered enormously. I put them back in the drawer where they belong. On a whim I tried some Rotosound 77 flatwounds, and whoah. It sounds bright, but not too bright. The action is still super low, and high-position chords still ring long and true. Mind you, each setup did take several days - in spite of the dual truss rods, the neck has moved on me a bit, but that could also be attributed to Arizona's rather extreme climate changes. I haven't been able to get the humidity in my room above 20% in about three weeks, so I can't attest to that aspect.
Basically this is a long, convoluted way of saying I wouldn't bother changing out the pickups right off the bat, unless you want to sink some (comparatively) serious cash into it. SX instruments are infamously unreliable between batches, so maybe I got lucky. I ran it through a Yamaha DAW into Cubase and the unaltered output levels were almost identical from string to string. Playing it through my Ampeg BA-112 (yay apartment life!) I haven't needed to move the EQ knobs more than three (hours? degrees? you know what I mean.) If you're dead-set on making major alterations to the tone, and if a proper setup doesn't get you where you need to be, I'd suggest starting with an Audere pre-amp. At least then, if that doesn't work out, you can slap it into another J. Not so with the Hippo's.