Re: Middle PU suggestions please
It is maple neck with rosewood fretboard, triangle inlays. The body is boxwood and is pretty heavy. Super strat look. I really like the feel of the guitar and the fretboard is one of the most pleasant to play I've ever touched. That is why I'm willing to put $ into it.
I don't know too much about pickups except I know what I like when I hear it. Should all three pickups be close to the same resistance, since there is only one volume knob?
I was going to go on about tone woods versus the money you throw into the guitar, but if you're sure you want it....
Boxwood? Agathis? Soft maple? Basswood? I'm not sure what box wood is, so I'll assume that the wood has no tone, sort of like agathis in a sense. I'd say try a Custom in the middle. I have no experience with it, but I think it's supposed to be close to a medium output humbucker, if that's what you're sure you want.
However, if you don't care about output (like the other guy responded) I'd recommend a Five Two middle. I have no experience with it, but I'd think it would have the best of both worlds, in the sense of not shrill on the high end (alnico II magnets) but tight bass on the low end (alnico V magnets).
The only single coil I have experience with is the Alnico II Pro Staggered single coil, and I don't know if it would sound like mush in boxwood or not. If the guitar sounds bright when unplugged, it should work fine with it, but I'm not sure. It worked fine in a soft maple body Ibanez I had, tempering the highs and giving it some mojo that it was drastically lacking. That Ibanez was rosewood fretboard, maple neck, and a tremolo tail, so it should be a lot like your guitar (except this one was H/S/S pickup configuration).
I'd call and ask Seymour Duncan's rep directly on this one, since I have no clue what box wood is. That's what I'd do, if it were my guitar. If it were maple, I'd go with Alnico II magnet pickups of some kind. If it were cheap basswood, Alnico V magnets. If it were agathis, Alnico V magnets or ceramic magnets. From there it's about how much output and what kind of sound you want in the various positions.