Have you thought about adding original Moon pickups? Talk to Danny from JapanBassDirect (or BassJapanDirect), and tell him you are looking for a vintage and original Moon JB pickup!
I actually have 2 sets of Moon MJB pickups and Blackbird Preamps from JJ-4 mod projects I've done. If you're interested send me a PM!
On the topic of EMGs, one thing I consider is whether I want pole pieces or a bar magnet. The bar magnet has a smoother attack which may or may not be something you like, and the results vary bass to bass.
The EMG JVX's are some of my favorite pickups out there. You get all the benefits of EMGs but with a more "traditional sounding" J bass attack. That being said, I just popped some EMG J-X's into a JJ-4 and they sound awesome!
Some people have had really great results with the JA/JAX pickups but personally I found them to be a bit dull. I am also personally of the mind that the X series is a vast improvement over the original recipe across the board. Happy to chat more about EMGs, I've tried a ton of them!