I have changed quite a few clutchs on 4.6's. You don't have to loosen the motor mounts. As for the Vibration, use some common sense. If it started after the new flywheel and clutch were installed, then there's your problem. Why didn't you just get the flywheel machined? Unless the old one was shot, you could have gotten it done by any local machine shop for about $10. DO NOT run the car with a severe imbalance like you have now. You will wear the main bears down to shreads. Good luck Bro!