From my personal experiences, I would recommend:
Seymour Duncan:
Neck: Lil 59 - I find the 59 sweet and warm.
Middle: Custom Staggered - Warm, takes cleans well, sounds good on distortion and has that fatness to the tone.
Bridge: JB Jr or Something else. Test the JB Jr (on someone else's guitar) before buying, it doesn't sound exactly like the JB and it's kinda you like it or you hate it. The chugs are really crunchy if you like it.
I don't have enough experiences with other brands to give you a good assessment. I would advise against mixing brands though.. doesn't tend to work well.
And again, seeing how close my recommendation is to the Everything Axe set, that would be my recommendation.