Yeah on a lot of guitars the bridge pickup will be setup to be closer to the strings than the neck pickup. The height thing is a preference, like Metaltastic said. You may have some wiring issues though, check the ground wire in the control cavity. Make sure all of the wires are soldered properly. I have a friend that bought a really nice JCustom from Ibanez about two months ago and all of a sudden his pickup selector is jacked up and causes the signal to go in and out completely when he plays. It's because of a shoddy switch and bad wiring. He was really disappointed in the wiring job they did...I mean, it was a $1,700 guitar, you just kind of expect the guitar to have good wiring when you are paying that much.
That said, I was having trouble with my neck pickup on my EC-1000 (EMG-81) and I was very disappointed when I looked at the wiring job and found out that the bridge wire was soldered to the battery cable, but the neck wire was merely taped together with the bridge and battery wire. Would it have been that much trouble to put one more bead of solder on there? Once the tape got old enough it just started letting go, which resulted in a really underpowered active pickup. I soldered it properly and all is well now. Really the wiring should be PERFECT in any guitar, regardless of how much...wiring isn't something that is difficult or anything. Just my opinion though...
~006
