Welcome! You will become very educated on pickups from this forum. Things to consider are the body, cap, and neck woods. Pickup hight and pole hight are extremely important and easy to tweak yourself to your taste. Of course your amp plays a large roll in tone (yours is perfect for what you seek).
For Opeth tone the Nailbomb or Black Dog would be my picks. Alnico V Nailbomb set will probably do everything you want here, and handle the very vintage metal tone Mastodon plays. It will give you pretty cleans as well, lots of warmth, great low end, and most importantly sound clear. Go to the BKP mainpage and check out the Nailbomb sound clips, especially the "progressive" and "clean" clips.
Another possibility is the Cold Sweat. It is a ceramic pickup and is more bright than the Nailbomb, but thus holds a very tight low end especially when detuned. Most notably is the beautifull cleans both neck and bridge produce. The Cold Sweat neck is a favorite among BKP users and is often chosen to offset a heavier bridge pickup. It has a beautiful liquidy solo tone.
Lastly is the VHII. I was going to suggest the neck as a possibility to the Cold Sweat bridge, or even with a Nailbomb bridge, but you could probably nail both band's tones with these by cranking a little more overdrive. Both Opeth and Mastodon don't heavily distort their tone anyways, and they definitely have a more classic and open than modern sound. The VHII was aiming for the "brown sound", and has one hell of a great classic rock tone that does metal pretty well. Many of the vintage lower output pickups are prefered by metal players in this forum because of the clarity, openess, and organic vibe, among other things. Even the Aftermath, one of the most "metal" pickups BKP makes is only about 14.7kz; not the highest output pickup by a long shot.
So with that, check out the clips, some here on the forum, or even youtube (good quality vids). There are more suggestions and I'll bet even Mules could work but probably not for your guitar, and for a more metal tone that gets Opeth/Mastodon, breathes fire, and gives you the dynamics you want then you can't go wrong with the Alnico V Nailbomb in a matched set. Good luck and happy tone hunting!
