I have personally replaced the main shaft, and center hub in thoughts that something may be bent. I have balanced and verifed the flybar is straight. And I have verified my blades are in perfect condition and balanced. Here is what I have found from my BCPPro:

1) on my heli there will always be a slight vibration at slow head speeds that corrects itself when the engine is getting more and more throttle

2) this slight vibration has no effect on flight performance

3) even if you blades are balanced nicks in the blades can cause a vibration as well as a loss of tracking

4) One time I had a vibration thought the whole body of the aircraft while hovering. This was due to a couple connections on the frame being pushed out and loose. Once I made sure everything was connected well it worked fine.

Hope that helps