1999 Mustang GT Vibration at 1000 rpm & clutch pedal vibration

Hi,
I have a 1999 Mustang that I just replave the 4.6l 2v motor in. At 41K a piston skirt broke. I have never driven the car before the Ford Remanufactured engine was installed. There are 2 problems.
Problem #1:
The motor has a vibration between 1000 rpm and 1200 rpm. Before 1000 and after 1200rpm it runs fine. I've followed all of the factory service manuals info but that didn't help. This vibration happen when driving and at a stop.

Problem #2:
The clutch pedal seem to have a fair amount of vibration comming from it. Some times it will be so grate that the pedal starts to make noise.

Thanks for any help that you guys can provide.

Robert