I'm definitely getting comfy now between the middle and neck pups - and I also found myself over the middle one as long as I was playing on the mid to low strings - and I moved up toward the neck a bit for the high E which is where my problem happens. So, it's just a matter of getting used to it.
But I love the Strat! I named it Alberta, but my wife nicknamed it Birdie (from the 'berta' part of the name). I like birdie!
Jim
James V. Signorile, ASCAP