I've never really been fully happy with any HSH configuration, personally. The closest was with a Suhr Modern with SSV neck, ML middle, and SSH+ bridge (the stock pickups). Somehow, the positions 2 and 4 sounded REALLY good in that guitar, even better than a '54 AVRI Stratocaster that I had (also stock pickups), believe it or not. So I ended up selling the Strat and keeping the Suhr Modern for a long time.
Anyhow I might not be much help with a pickup recommendation, except that I think that you need to decide what you want the middle position to be for. Other wiring might also play a part in what you choose, like in the in-between positions are you coil splitting the humbuckers or not? Suhr and some other manufacturers do some wiring tricks (you can find diagrams online) where the humbucker sees a full load from the volume and tone pots, but when you switch to the single coil it sees half the load (typically you want 500k pots for humbuckers and 250k pots for single coils). I'd suggest one of those wiring tricks whatever route you choose, maybe just look up the Suhr Modern wiring diagram as I was extremely pleased with that sound.
I don't exactly know which single coil to recommend you, maybe a True Grit? Personally I would get one that's a little bit hotter than a normal Strat, but that still sounds very Stratty. I wouldn't worry about it keeping up with the Nailbombs (which are pretty high output), I would keep it for when I wanted a more traditional Strat sound and maybe step on a boost or something if I needed to worry about volume loss in a cover band situation or whatever.
You kind of have two choices in other words: try to go high output single coil to keep up with the Nailbombs (in which case you will lose the Stratty tone), or just deal with the volume loss and keep the Stratty tone. I prefer the second route.
