I am saying this by some experience. I am saying if the heli wasn't vibrating before in flight without the fuselage.. Then head speed is the issue.
I saw this first hand with someone at the field. He installed a fuselage on his heli. Maidened it and man did it vibrate! He lowered the head speed and it went down. A lot! I also have read about it sometimes.. BUT!
BUT! If I were you, I would do exactly what tony and lee are saying, check everything and balance everything very thoroughly! Maybe If at all possible, try hovering the heli without the fuselage. Fix it, make it perfect, and then put it back in..
If any shaft is bent and if any thing is wrong with the boom like tony and led ate saying , you need to fix that ! Right away. First... After that if you have vibrations in your heli, try the headspeed thing. Won't kill it.. And not drastic lowering .. May be reduce by 100 rpm- 150rpm lesser. Your heli will become less responsive to inputs.. Softer on the sticks but that's what you want with scaled fuselages.