I do not like the JB. To me it sounds like the guitar would have been played with a pick made of glass or something. It has a strange spiky sound (upper midds) which you just cannot dial out. OK sound if you use über-scoop sounds, but then again you are on the mud-zone.
I used to have EMGs (707 and 81-7) in my guitar, but I just couldn't get the sound I was after from them. They sounded like a sack full of bees. Very plastic-like sound - Unmusical and lacked in personality.
For last three or so years I have been using Lundgren M7 in bridge and I couldn't be happier. Percussive and really punchy sound. Responds very well to picking and volume pot fiddle. I love the palm mute sound of this pickup. I am going to have M8 on my 8-string, which should already prove that the bass responce is not muddy at all, but still remains huge.
Bare Knuckle pickups are flaming great as well (at least the 6-sting ones. Are there also 7s available?).
Have you experimented with different PM techniques? By the PM techniques I mean how hard and from where you press/mute the strings?
Sometimes when I want to get really tight and agressive sound I PM rather hardly and "far" from the bridge. That way I am able to get really agressive and percussive sound which truly cuts through. I use this kind of PM especially if I am playing something like Fear Factory (i.e. Shock).
Works well with both, actives (at least with EMGs) and passives.
Also, do not expect to be able to get heavy tone if you are just gently touching the strings. Sometimes guitar needs to be employed as a percussion instrument.
Like already about million purist guitarists have stated: "The sound comes from your hands and fingers - The rest is just crap to disquise that one is not able to play well".
However, in contradiction to the statement, I am helpless gearhead, but still find that sentence to be the essence of all playing.
Anyhow, it is again the notorious question of personal preferences, thus none should begin to crucify me because I did not like their pickups or something. It seems that this is a major problem in all forums - people just take everyting too seriously and parsonally.
All the best