I've got a killer LTD M-1000 (Alder Body, Maple Top, Maple Neck, Rosewood Fingerboard) but I'm not a fan of the pickups. I want to get some nice passives for it.
This guitar would be used for progressive metal (Periphery, Haunted Shores, Veil of Maya, Tesseract, The HAARP Machine etc.), so it needs to be really tight, really clear, and have great cleans as well. The neck pickup needs to be clear and articulate, not saggy, not thin. I like when there's a very clear pick attack on the notes too, where you can really hear the pick and string interacting. With the bridge pickup, clarity is extremely important, but I want it to still have lots of midrange. I also play it in Drop C.
Crunch Lab in the bridge, and a Humbucker From Hell in the neck. Or the Full Shred set if you want Duncan.