I worked out almost everything and I'm now down to my last setup concern.
All the volume and tone knows are the same except one. For some reason the bass volume knob rotates quite a bit further than the others. For example, if all the other knobs go to 12 o'clock, the bass volume goes to 3 o'clock. The other weird thing about this is that once it goes past that position, it's as if it's ever so gently rubbing against something underneath.
When I solo the neck pickup and turn it, it doesn't feel like much is happening here. However, when I have both pickups on and I turn the bass volume past that threshhold, I experience a small dip in output. This is making me very uncomfortable.