I have the JB and Jazz set in my main guitar. I have found pickup height to be the most important part of getting the tone I want. I live in Tucson, AZ, where the summer is hot and sticky from monsoons. During this time, the neck is constantly moving, changing string height by up to 1 mm when the weather changes are extreme.
By noting the height from the strings I desire to use, it takes a minute or two with a screwdriver and metric ruler to find the sweet spot again. If I pick it up and it sounds like crap, this is usually the problem. I also usually have to change, or should change, string height and adjust the truss rod once or twice a week to maintain the feel I desire. All of this stuff is written down and the tools are always at hand to make adjustments when necessary.
To apply this a little differently, if a person uses a pickup and it's producing too much of a particular, broad range (bass or treble, for instance), either raise the opposite side by half a turn at a time or drop the offending side by half of a turn. Do either or both until the sound is to a person's liking and write that down, measuring from the bottom of the 1st and 6th strings to the top of the pickup. This is a free modification and will even improve cheap, stock pickups.
In general, the treble side might be 1.5 mm to 2 mm and the bass side seems to sit about 2 mm away with most of my guitars guitars, including EMG pickups. Any difference from that is usually due to moving the bass side away by up to .3 mm to improve clarity. Sometimes, when I want less drive and compression, the pickup is set a little further away, about 2.5 mm on both sides, but any further than that begins to impair signal-to-noise and the sound loses body. So, if a person finds what they like, being precise pays off.
