To replace the too-warm stock single coils, I ordered a set of GFS 60s-70s Greybottom Non-stagger Overwounds. These were a really good deal; about $70 for the set, and they made a noticeable difference to the sound of the guitar: way more sparkle and punch, and pretty similar output.
But the Atomic II humbucker still presented a problem; it's a high-output pickup, way louder than the single-coils, and I think really optimized for driving a high-gain amp. As much as I like that, I wanted a decent clean sound too, and I found the Atomic II to be too midrangey to really be likeable clean. After reading many, many reviews, I decided on a Seymour Duncan '59 (the TB59 model that has the right string spacing for the strat, although I gather this doesn't really make much difference, and the regular SH-1 model works perfectly well too).
Right away I thought the '59 was a better match for the guitar. While still considerably louder than the single coils, it was at least closer, and the clean sound was quite a bit nicer: a better tone curve overall. But, I still wasn't happy. Even though the '59 sounded pretty good into my old tweed fender amp, I thought it sounded a little on the muddy side, especially noticable when I switched from the middle single-coil to the bridge humbucker. Reading everything I could online, I began to suspect that the problem was that the humbucker is still coming through the same 250K pots that strats come with. Gibson generally fits its HB-equipped guitars with 500K pots, which lets more of the high-end through. This is apparently especially true of the volume pots, which have an effect on the resonant peak frequency of the pickup.
So one solution would be to change the volume pot in the strat to 500K. I considered this, but reckoned Fender chose 250K pots for the strat for a reason; they might become too bright as a result. Plus, I thought it would be nice to be able to control the volume level of the humbucker separately. Why not re-wire it to have two volume controls instead of one? I would gladly trade one of the tone controls (which I almost never use) for a second volume. Then I would have a 250K volume for the single-coils and an 500K for the humbucker—which is what they were designed for.
Seems like a reasonable thing to do, but if you try Googling this, you will find almost nothing in the way of advice or wiring diagrams. The only thing I found was this article at GuitarNuts... with the caveat that it was only a diagram; they hadn't actually tried it. Seems nobody wants to go this route... two volumes on a strat. Go figure. Well, I thought I'd try it anyway.
Working from the GuitarNuts schematic, and staring at it for a very long time, I realized that the tricky thing is to isolate the two volume controls; if you try to wire it up anything like a regular strat with a 5-way switch, you end up with the two volume pots in parallel. What you need, of course, is one or the other, not both. The GuitarNuts schematic suggests wiring up the 5-way switch in a completely different way than the usual: you isolate the two halves of the switch (and for this reason they emphasize that this mod is only possible with a true 2-pole switch—I got mine from Stewart MacDonald). You use one side of the switch to bring the hot wires from the pickup in and route them to the different volume pots. You then use the other side of the switch to route the different pots separately to the jack. There is no wire that connects the two common terminals, as most strat wiring diagrams show.
After a lot of staring, a lot of soldering, a lot of testing, and a lot of mistakes, I achieved what I wanted. Here's what I came up with (click for a bigger version):
This is a little different from the GuitarNuts version; I wanted a 500K tone pot for the humbucker alone, and no tone on the single-coils at all; their version had a common tone control; I can't say if that complicates things or not, 'cause I haven't tried it.
In my diagram, you'll see the hot wires of all three pickups coming over to the one side of the switch. Then, the green wires run to the two volume pots—the common terminal leads to the 250K for the single-coils, and I'm going straight to the 500K from the humbucker. The tone control is wired in the straightforward way that a single humbucker gets wired; nothing fancy there.
The yellow wires in my diagram lead back to the other side of the switch; note that there's a jumper connecting the neck and mid poles. The common terminal on that side of the switch then provides the hot lead out to the jack (in red). So, when you set the switch in position 1 (or whatever), you're not only setting which pot the pickup connects to, but which pot the jack is connected to. This is what provides the isolation between the two: it's as if you've got two switches instead of one.
You may notice that my 5-way switch looks backwards compared to the wiring diagrams from Seymour Duncan and other sources; this confused me too until I simply figured out which were the common terminals (the ones closest to the centre) and went from there.
I've shown everything connecting to ground just to minimize the number of lines in this diagram; in the guitar, there is a common ground wire that connects all the pots, and all the pickup grounds come back to the pots too. That makes for a messy drawing, though.
As I say, this works. The 5-way switch works in the usual way with positions 1,3,5 giving you each pickup and 2 and 4 giving you B+M and M+N. But the volume controls are separate; one controls the neck and mid; the other controls the bridge. I position 2, they both work, and the sound is kind of thin; not a position I go to very often anyway.
The sound of the humbucker, though, is pretty much exactly what I was after; it sounds bright and full, losing some of the muddiness it had through the 250K volume. It sounds much better as a match for the single-coils, and I can set its volume to about 8 or 9 for a better volume balance with the other pickups. Or crank it up for full gain. Really, this achieves what I had really wanted out of a bridge humbucker, which is a fatter, fuller alternative to the usual strat bridge.
Hope this helps you.