Oftentimes, the best TONE is not the most DISTORTED one. Distortion masks a lot of the natural tone of the guitar itself, as well as compressing the dynamics out of it.
Fortunately, most of Tim's pups, even the really high output ones, have great clarity for clean stuff. Some are tighter, darker, more compressed, more open, etc etc.
A Miracle Man/Cold Sweat would be a great metal setup, while still being able to do good cleans and a nice, balanced middle position.
For a more PAF-ish sound, as HTH pointed out, you would want to go with an alnico-based pickup, and something with more dynamics and less drive. You might want to consider something like a Black Dog/Cold Sweat setup, or a Riff Raff/Cold Sweat setup. My notes attributed the basic tone of the Riff Raff as "Classic'. To me, it's got the quintessential 70s rock humbucker tone! The VHII is more open and a set of VHIIs makes for a really well-balanced, versatile set that you can do metal with if you dig in hard enough. The Black Dog is also on the brighter side with a really clear midrange cut.