Doug's Headers installed with some clearance issues

If you were to shim the mounts about 3/8 of an inch on both sides your problems would be gone. If you look at the pics you posted just loosen the motor mounts, grab a block of wood, raise the motor just a touch and you will see the needed space appear in those tight spots. That is what appears to be wrong on your car. Them motor mounts have the whole front of the motor sitting just 'that much' too low, good luck,
Chas