Pickup ideas for future guitar build

[Miskatonic]

In the brainstorming stages of a Warmoth guitar build.

Here's some info.
VIP Body shape
Chambered body
Mahogany body wood, quilted maple top
Recessed original Floyd Rose
Bridge and neck humbuckers
Rear rout, 1 volume, 1 tone, 3 way switch
Binding on top

Warmoth pro angled neck
Mahogany "Warmoth" shape
Ebony fretboard with binding
10-16" compound radius
6100 (Jumbo) frets
Standard thin (standard Strat or Tele neck contour)

The finish is red dye on the top of body, solid black gloss on the back/side, neck and headstock.

This is primarily a metal guitar, but versatility in pickups is always nice. I like good crunch with articulation and just the right amount of bass. Definitely not searching for a Vai or Gilbert shred tone.

Here are a few songs to get a general idea. Both rhythm and lead tone.

http://www.youtube.com/watch?v=h-dlejnCCig

http://www.youtube.com/watch?v=4yFvfe31cC8

http://www.youtube.com/watch?v=a7C9Tr4okNw

http://www.youtube.com/watch?v=mxxYRuilMmk

I like death/black metal but a lot of the time I find the rhythm sound tends to get a little muddy (Opeth at their heaviest is right on the edge of that but still clear enough), especially when playing something more complex. I know that most of the bands tune down their guitars quite a bit but I'd like to hopefully stay in standard tuning and just let the guitar and amp provide the tone I want. I also really like the guitar tone on Master of Puppets but it is missing some of that punch that the "modern" sound has.

Right now I have a Marshall 8100 (Chuck Schuldiner R.I.P.) and a Mesa stiletto straight cab, but I've got my eyes set on a used 5150 when I have the cash.

Any suggestions are greatly appreciated and let me know if I've left out anything.  8)

[Miskatonic]

Leaning towards calibrated warpig set.

[Nolly]

Apart from the Opeth track, the tones you've referenced would all be very well served by a Miracle Man. The Nailbomb is arguably the best choice for the open and crunchy tone Opeth go for (hence the addition of the 'Progressive' clip for the Nailbomb's page on the BKP website).

On balance I think a Nailbomb would probably be a strong choice for you - it's got enough punch for all of the extreme metal tones, and in E standard it shouldn't have any issues with tightness.
However, another pickup worth considering would be the Aftermath, which is definitely on the smooth side for a ceramic pickup. It also has a very aggressive and crunchy midrange, and has a satisfyingly uncompressed dynamic. It's lean low end makes it phenomenally tight.

[Miskatonic]

After doing some looking around and taking your advice into account I'm thinking maybe an Aftermath in the bridge and a Miracle Man in the neck.