On the subject of coil alignment, I bet some kind of very dense non-reactive fluid suspension would help. Of course, that would be expensive as ****, hard to design, and a hell of a lot more complicated than your average SPL woofer. It would be cool as **** though.
I'm not sure exactly how subwoofers work but another idea would be a magnetic field perpendicular to that of the coil, with a functional radius small enough to keep the coil away from the gap. Kind of like how particles in a super collider are kept in the center of the accelerator.