Don't worry about distances. If the neck pickup is where you want it (tone wise) then set the volume controls to be the same at lower volume say 2 or 3. Switch between the two pickups and strum a chord. If the bridge is is louder then lower the bridge pick up until the same volume is achieved between both pickups.
Another way is to mark where the bridge pickup is now. Lower the bridge pickup down until it is even with the top of the ring. Play your guitar and and raise the pickup until you find the nice spot. If you find it, then check the balance between the two. There are a lot of variables, but it is nothing to try and it is amazing how good you can get them to sound by adjusting them. Also you can adjust the pole pieces to match the radius of your fret board. You can cut the muddiness by lowering the bass side of the pickup. You can balance the bass by burying the low E pole piece. It just takes a couple of screw drivers and playing around. You are not going to hurt anything. Hollows and Semis can be helped a lot by lowering the pickups.
Lastly - if you don't get something you like - you can always change pickups. :shock:
Also - I am no expert, but I did stay at a Holiday Inn Express - once. :mrgreen:
Edit spelling, clarification