Hi,
When you run each pickup seperately do they sound alright? If the output is low when you are running two pickups then it might be 'insertion loss' (which I am trying to solve right now).
I remember my neck pickup was louder than my bridge pickup but when i rolled in the neck volume the overall output would decrease.
If it is indeed a very bad case of insertion loss, then you might look into getting one of these to replace your volume control(s)...
http://www.emginc.com/products/index/206/147/4
hope this helps.