Mine was like that too but You just gotta working on it
Of course the doors are first but don't forget the alignment at the top front of the door to the
bottom of the windshield post. Look at other E-bodies and make yours the same. then the bottom
of the door, then the fenders, don't leave the little bracket under the top of the fender off even my
fiberglass fenders have that bracket.
you have to make the engine bay a square hole to match that hood with a tape measure and lots
of time with only the outer four bolts on the top of the fenders to start and don't do any hood aligning without all the hood bumpers and springs in place.
Shims should not be needed in a perfect world but since we don't live in a perfect world you might
have to hide a washer here or there to make it right.
You have the extra problem of the shaker but those never did line up very well from the factory
so you might have to fudge there too.
Now if this car was ever in an accident or on a frame machine your job will be that much harder
but try to get help 'cause 2 pairs of eyes are better then one
Don't forget to spend extra time on the passenger fender because they seem to droop a little down
for some reason when looking straight from the front