The starter has to be out before the cover can be bolted into position and make sure the "lips" on the cover engage the rear edge of the oil pan.  You will find it easier to disconnect the left motor mount and raise or "tip" the motor to give you the clearence to slide in the header, easier from the bottom before the clutch z bar goes in.
 
Bob
A.C.E.S. #1164
T.C. #375
65 Malibu
65 Malibu SS
85 El Camino
96 Camaro

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