I'm not sure how old this thread is, but I'm adding input regardless! Merry Christmas by the way :)
being a Painkiller user for 4 years now, and with experience using the Warpig, Duncan Sh-6, and Duncan Sh-10 (full shred), maybe I can offer some insight from personal experience. I jumped on this forum because of my new found desire to try the aftermath. Of course, the Cbomb has always had my attention as has the MM.
I think, OP, that you might need to consider looking into higher end amplification. I mean, if you can't find incredible metal tones with the Painkiller or the Aftermath, and think that the Duncan D is somehow better... well, I dunno. I've owned the marshall amp you have, and it is not anything near what it should be. I play through a KT88 loaded Framus Cobra now, and its EVERYTHING it should be... and much much more. If you are addicted to the 2000, can I suggest you send if off to FJA Mods for the upgrade that amp needs to shine? Otherwise, sell all these pickups and start fresh with a new amp! Of course the Duncan D sounds good with that Marshall, they are both at the same mid grade level in the tone world. And that's fine, and even more so, maybe you should just stick with them! though, I feel that you might be looking for something in a pickup that you'll need to first find in a quality amp. And lastly, pickup height is HUGE the BKP's I've owned. Like the one djentleman stated, a half a turn on the adjustment screw is night and day.
As for the Aftermath, I'm looking for a little less high mids and a little more low mids, and perhaps a bit more tightness in the lower tunings (drop C to drop A). The Painkiller sounds fabulous, and I might just leave it be. But the AM has been callin' my name for months now..
lastly, have you tried the duncan full shred? its an incredible thrash metal pickup.. it has it all, and its alnico V. Just don't go below drop C# with it. People have no idea that the sh-10 is perhaps one of Duncan's finest achievements.