I like the stock Jaguar pickups as/is, they sound perfect for me, which I admit, can be kinda weird coming from one of the more "metal" people here.
However, I bought my CIJ Jaguar around this time last year for $640 sound unheard with plans to return it to stock, and wound up finding that the so called "Hot Rails" that were installed in it were really Seymour Duncan SCR-1b bridge position Cool Rails. They sounded so darned close to the apparently hot-wound stock pickups in the vintage Jaguar I played years back, so I stuck to them. Besides, they have an extra benifit to get a broken "Hy-Lo" cheap-o guitar tone when one coil is cut off from the mix.
Interestingly, when I added a set of "cut-off" Jaguar pickup covers to the cool rails around June of this year, I found it difficult to get the bridge pickup close enough to the strings with the neck shim installed, so I took it out, and man is this guitar alive and full of sustain now. The neck pickup is set a little lower than the bridge to counteract both pickups having the same output. I plan to add some claws sometime in the not so distant future.