Usually the tradeoff with humbuckers is they're less bright, and the QP's are already considerably less bright than standard issue vintage single coils. So you likely wouldn't notice as much difference than if you have regular vintage style J's. But it depends on a lot of factors about the pickups themselves, not just humbucking and single coil, so YMMV.
I'd be looking to something weird in the preamp before I looked at the pickups, though. Pickups don't usually just go bad, and QP's are built solid. Parts in preamps are more likely to be a problem IMHO.
Ampeg Portaflex Club #1