Re: pickups for filling mids?
The problem with the JB is that's a VERY bright pickup. It's supposed to be pretty-near orgasmic in mahogany, but in alder under a maple cap... you've got more treble than you need there, especially if you're going for holdsworth, santana, and EJ.
Another thing to note is that the first two guys are both known for being Mesa players, and while Johnson isn't, I agree with you- I'd say a Mark-series is about the quickest way to his tone you're going to find in a single package. Are you sure a Marshall is the right amp for you? I owned a TSL that I sold for my Nomad for the same reasons- I wanted soemthing smoother, withoput that sizzling "crunch" in the upper frequencies.
Before you go overboard with pickups, run down to your local mesa dealer and plug into a Nomad (vintage mode) or a Mark-IV. You may find the EMG's actually work quite well with the right amp.