I know a lot of guys on OSG use the Novaks and Lollars.
There's also a Canadian company called PIckup Wizards, not sure if they do Jaguar pickups, but my Jazzmaster has one of their hotter wound pickups in the bridge (8.8K, Alnico 2 Magnets, it's a fatter sounding, slightly more mellow Jazzmaster pickup).
With a Jaguar you are never going to be able to get too far from the Jaguar sound though, the unique bridge and tailpiece are a part of what makes it sound the way it does. I have a pair of Seymour Duncan Cool Rails in cut-off JAguar pickup covers with the claws installed and 500K pots in the lead circuit on my CIJ, and while it sounds thicker and warmer, and does pretty good for the Hard Rock and Heavy Metal I play, it still sounds like a Fender Jaguar, and still has that surfy-quality to it, with a little less sustain, and that 'tchack' attack sound Jaguars are known for. With that much tweakage you'd think it'd sound more like a Les Paul, but it rather well doesn't, though I can "dial it" into more Gibson-like territory if I'd like, it does a great Def Leppard tone.
Best best is something with an Alnico 2 magnet and slightly overwound for Jazz and Blues, that could put you in the right territory, I think Novak could do some custom pickups, or even fix/re-magnetize the old ones if the magnetics are all that is wrong.
