Try the JB with a 300k pot.. i think a lot of the So-cal alder strats/maple neck were shipping with that and i thought it was fantastic in the guitar I had. Mind you the lack of a tone knob made the pup slightly brighter so a 250-300k pot probably is the sweet spot in that configuration.
The SD distortion is fatter than the duncan version. It has smoother highs, is hot, fat but tight. It's a great pup for a brighter guitar and you don't flub on the low end.
Custom custom SH-11 - not a fan of this pup at all. Love the smooth highs but the bottom end is loose as all hell. Even in a brighter guitar, I just didn't have the tightness in the riffs.
Maybe try the Dimarzio AT-1? Supposed to be tight but a little less sharp on the ears like the JB is. Some have compared it to a JB with a 250 k pot so maybe that is the solution for you if you have a shared vol pot (which most of us do in strat type guitars)
If the tonezone is too big sounding and artificial, you might like the air zone. It is probably what the custom custom wants to be.. tight in the low end.