Why does my W8 4Motion (6 speed manual) shutter while accelerating after 1 hour?

What is your question?

The problem always happens after being on the freeway for over an hour and continues at slow speeds and in 1st through 6th gear after I get off of the freeway. After the car has been parked for a few hours the shuttering (shaking) problem goes away. The engine seems to be running fine. Could this problem be drivetrain related? The engine has just been professional tuned and fuel filter has been replaced. Transmission was rebuilt 5,000 miles ago.