I swapped the stock pickups (custom neck, D-Sonic) in my JP6 with a set of Alnico Bareknucle Nailbombs and I'm pretty happy. A bit more responsive to volume and attack, and more of a vintage hot flavor, especially in the bridge.
That said, you can pry the stock custom neck from that JP6 out of my cold dead hands. I love that pickup, and even though I'm not using it, I'm happy to have it. I know it's essentially an Air Norton, but it's MINES.
Also, I don't know that I'd swap the pickups out of an Axis. Every time I've played one, I've been pretty happy with the stock dimarzios