I haven't done too much experimenting with lots of different pick ups (I haven't had the privelege of owning tons of guitars) but I remember with a strat that I had and couldn't get a very clear tone out of the neck pick up, I experimented a little with the pick up position. Just raising the pick up ever so slightly beneath the top three strings, and lowering it slightly beneath the wound strings. The nice thing is that it's a real easy solution to try as you go - no taking apart the guitar, messing with something, putting it back together and testing. Play and listen as you tweak. Even if it doesn't clear up the muddiness it can help you dial in a more personalized tone pretty quickly and easily. (This whole comment probably goes without saying for most people on this board.)