I use the ahb3, Mick Thompson emty Blackouts in both of my explorers. Both tuned Drop B. They are not muddy whatsoever. They are my favorite active pickups ever.
Now I did have a set of the regular ahb1 blackouts in one of my explorers for a while, they are inherently dark and bottom fat pickups. (Which is why they have revamped them a couple times)
I did find them a tiny bit muddy. But.... They are what they are at any tuning.
I'm curious which set you have? Edit: I looked it up, you have the Ahb1 pups.
Also.... Given the output of those, I would also suggest you can drop the bass and increase the mids and treble on your amp to compensate quite a bit for that.
In my head I know Jackson matches their pickups pretty well....and.....most people are buying 7 strings to drop to crazy low tunings.... Those pickups were made for drop tunings. It's gonna sound fine.
Nice friggin axe by the way!