Pickups don't really have all that much to do with sustain. That is more of a factor of the wood and the hardware involved. The adjustment of the pickups can make a difference in the sustain, because if they are too close they can suck the energy out of the string, but that will happen with any pickup.
For myself, I always find EMGs to be really stale and sterile. They are very clean, and there is no question they are the quietest pickups you will find, but I just always find that they have no character, no personality. The JB has character to burn, and is the pickup I would choose. The additional benefit of the Duncan is that you don't have to replace both of them at the same time. The EMGs will not work with other pickups, as their impenitence is much lower.
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