Troubled neck

I just built my first Pit Bull. It's a 6 string bass. The neck has a rattle inside that I've narrowed down to the the lower register truss rod. The neck is not slightly back-bowed so it comes flat under string tension, or flat, so it has a slight up-bow under string tension. The action at the high side of the neck is too high even with the bridge set as low as possible. Shimming the neck joint to change the neck angle helps some but then the neck does not line up to the top of the body face. Is it possible that I got a problem neck from the factory? Any suggestions