The Jaguar is naturally a very bright guitar, because of the 1meg pots and bridge. Humbuckers are always naturally warmer sounding. You def have the strangle switch turned off? 😉
Also you say with distorted you hear everything breaking up, yet you installed extra hot pickups!!
before upgrading your amp i say get a pair of Fender Jag AV pickups (about $90 for the pair), ive heard mostly bad about the SD jag pickups - i.e. theyre not very jag like.