My experience with anything tuned below D is to make sure the mids are bumped, or you end up with a boomy mess. It's why Ric 4003's sound so good through driven tube amps. Be careful with 'hot' pickups because they often lose mids and end up scooped (see Duncan Quarter Pounders).
Another option would be to wire your pickups in series, or at least with a series/parallel switch. Bumps mids, adds clarity at lower registers, and sounds great pushing tubes hard. Even if you pay a tech to do it, it should still be way cheaper than new pickups, and will have a greater effect on tone.
All that said, to me, the secret to a satisfying heavy doom tone is power tube distortion. Were it me, I'd ditch those guitar pedals, get a cheap tube amp of some description (Traynor YBA-200 can be fantastic for doom if you figure out the tone stack, and I paid $350 for mine used at a store), and dime the volume knob, adjusting gain to taste. With that much distortion, the finer points of different pickups won't matter much anyway.
Of course, lots of players have figured out great tones with cheapo gear that nobody else wanted (Boss FZ-2 fuzz and Electric Wizard, anyone?), so whatever, just experiment...