TTI Header Knocking Against Torsion Bar
Like said above check the condition of those motor mounts. I run a Schumaker torque strap on mine and it holds the engine in place without transmitting vibrations. Plus you can adjust the torque strap to move the engine slightly to "adjust" header clearance.
Did you check the engine position according to TTI install instructions? Engine must be sitting according to instructions or headers won't clear.