Yeah Im actually doing the same search man seeing as how I have an S520EX and Im about to grab a used
S540LTD.
There are a few pickups that I keep coming back to in my search, through personal recommendations from guys at multiple music stores, to searching the sites of DiMarzio and Seymour Duncan, to people on this forum.
Those are DiMarzio Tone Zone or Air Zone in the Bridge, and Air Norton or PAF Pro In the Neck. I can't really comment to much on the middle pup since my current main guitar is a S520EX w/ an HH config, so my search has not included HsH, but after a quick search on Dimarzio's sites it looks like recommended choices would be Chopper, Fast Track 1, or Air Norton S, plus I have heard plenty of people with S540's use the Air Norton, Red Velvet, Tone Zone HSH setup. So much so that when I had this conversation with the guy that sold me my S520 he scoffed at me when I brought those pups up, and said "man every one has done that already".. do Evo's or evo 2's. But plenty of people have dont that too so, I dunno. lol
Now as far as Seymour Duncan a 59 in the Neck and JB bridge or Jazz in the Neck and Duncan Custom or Custom/Custom in the Bridge are also great choices too, for maybe a little less output and a little bit fatter a sound than DmZ.. especially into a high gain amp.
either way it really depends on what your aiming for in the end, and more importantly what your plugging into. the stock pups in that guitar may sounds great on one and amp and not so great on another, and the same can thing applies to your guitar with new pups as well, ya know?
But I'm pretty much looking for the same thing as you, so I'll let ya know what I come up with and you can do the same. the only major difference between you and I is that I am looking for a pup configuration versatile enough to go from classic rock/metal to Jazz/Bluesy since my practice-for fun playing is reminiscent of my teen age years, while my studio playing tends to be for Hiphop/Rap and RnB records. Lots of half dirty mute picked dark sounding licks.
anyway hope this helps a bit.. lets see what we can come up with!
Jay