I respect what you are doing, well done for being open minded. I've also done the same as i love the Jaguar but find myself playing in heavy(ish) bands all the time.
Unfortunately CIJ pickups are not wax potted so if you use anything more than light Overdrive things get untidy. They can work for noise rock but they are not great for anything with discipline or traditionally driving valve amps.
Basically i have three Jags. One is vintage that i want to keep pure, the second is a sunburst CIJ that i upgraded the pickups to a seymour duncan Quarter pound (for Jaguar) in the bridge position and a DiMarzio YJM in the neck position. Thirdly i got a CIJ burgundy mist model specifically to 'hotrod', i fitted a DiMarzio 'The Breed' humbucker in the bridge position and a seymour duncan Vintage (for Jaguar) in the neck position.
Seymour Duncan upgrades do sound smoother with Distortion and are much quieter in operation than the CIJ pickups.
The Seymour Duncan QP (is the hottest available) in the bridge just about copes with 'rockier' styles and because it is designed for the Jaguar it looks right (with the 'Claw' and cover on). Be carefull with stuff like Hotrails and the JB Jr because they are not designed for the Jaguar you cannot fit the pickup cover over them afterwards and the Claw can be difficult, so the guitar does not look correct.
BUT if you really want Metal sounds, especially low end riffage you will need a humbucker OR use an FX Processor that will let you shape the EQ and Distortion.
I prefer single coils in the neck position anyway, so i just upgraded them with better quality pickups.
