Sounds like you've kind of made a decision about the pickups that you want to put in a really nice incarnation of the Strat. I've played one of these and I like the lightweight, thin body. You say you want to play metal on this guitar and in most cases, that calls for the use of that bridge pick up (especially if you are playing leads) and even still, if you are chunkin' rhythm and power chords, especially if you dig into the Slip Knot, P.O.D., Staind genres, you'll want a dark mid/neck combo sound. Let me suggest this set up for you:
Neck pickup-JB Jr 1N
Mid Pickup- APS-1 Alnico II (for your clean sound)
Bridge Pickup- JB Jr 1B (for your hi-gain lead attack)
The Jb Jr is an excellent choice for a hot output pickup that will fit in a single coil space. This requires no physical mods to the guitar (and I'm not sure whether the Aerodyne body is routed specifically for single-coils or is it a "bathtub" route like many of the Standard Strats) Using the JB also gives you the option of "coil splitting" so that at the flick of a switch, you can still get a really basic Strat sound. Now if the Aerodyne is "bathtub" routed, I'd change the pickguard out to one that's cut for a full sized humbucker and run an SH-6 distortion Humbucker to make this puppy scream. I've got a similar set up on my PT (you can see it atArchie's JBP PT with Duncan's Equipped )
You can also hear this guitar on the song "Blow Fly" at my site. Hears the link:
Click on the link to "Blow Fly" and hear the Duncan Pickups in action