What would be the difference in tone? I'll be buying a bare knuckle Nailbomb for distortion, and a bare knuckle Juggernaut for clean. I play a lot of metal, by the way.

I like my cleans very warm but with good highs still.
Examples: (Remove the spaces)
Intro - [forbidden link] .com/watch?v=de6VjUe0yNw

[forbidden link] .co.uk/main/downloads/soundclips/humbuckers/contemporary/juggernaut/juggernaut_-_clean_demo.mp3

When it comes to distortion, I like a bit of everything, but mostly good mid and highs (I like to leave most of the bass where it belongs... to the bassist :P)

The first video I posted might be a good enough example already, but here's another example just in case.

[forbidden link] .com/watch?v=sQ5-NbE09vo

So my main question here would be this: What would be the best pickup position for cleans, and for distortion? Neck, or bridge?
If you don't already know what you prefer then I really don't think a pickup change is going to do anything much for you at all.

A pickup change is a very subtle change in tone, even through the best amps, it's not going to suddenly make you sound like bulb just because you're using one of his pickups.
R.I.P. My Signature. Lost to us in the great Signature Massacre of 2014.

I like to use the neck for cleans, but that may just be preference. I find myself a little further from the bridge when strumming.or plucking.
But, yeah, a pickup is going to give you the smallest possible change in tone you can get. An aggresive pickup will not make a lesser amp sound any better. Which amp are you paying on, by the way.
Harmony: Stratocaster
Alvarez: F-200
Schecter: Omen 6
Fender: BXR-60
Dean: Metalman Z Bass (Betty)
Egnator: Tweaker 15
Pearl: Maximum
Custom: Harley Quinn Bass
Custom: TK-421 Explorer
A steadily growing supply of pedals
Bridge for Metal, Neck for Blues.
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Originally Posted by Tulkas
Stairway is required on any list of anything involving the words guitar or song, I believe Congress amended the constitution in order to put it into federal law.