2001 Ford Mustang vibrating engine

I just recently had a used motor put into my car. Iyt came from a close friend who had a standard. We put the transmission and other parts attached to the motor and now the car will start and run but there is a horrible vibration through out the car. I brught it to a local machanic shop and all they can tell me is that the vibration is an internal prioblem in the engine but the engine was working before I bought it with no problems. Do you know what may be causing the vibration?