You need to adjust the hood hinges on the inner fender upward, and then snug them just tight. Then lift the hood and loosen the rear bolts and rotate the hinge as viewed from the side, tighten the bolts and check the fit. Repeat until you get the alignment right.
Trust me, it sound wrong, but until I did it, the rear portion of the hood was 2 inches too high. I even slotted the holes in the hinges.
So the secret is to raise the front of the hinge on the inner fender