The inner wheel fender wells are bonded to the front quarter panels (the nose shell). If the inner fender wells are not correctly positioned before bonding, the hood will never fit correctly. The reason the hood will never fit correctly is because the hood pivot brackets are bolted to the inner wheel fender well pieces. To do it correctly, I think the procedure is, before bonding, to bolt the hood to the inner wheel fender wells, and then move the inner fender wells up and down, back and forth, until the hood exactly matches the nose. Then bond the inner fender wells.
When I bought my 68 Corvette, it had a terrible repair job, and the hood, like in the pictures was grossly out of position. The front clip was removed, the inner wheel fender wells removed, and all rebonded. The reason for removing the front clip was to repair other damage.The entire front of the car was a Bondo sculpture. .... Forget what I paid. T Wasn't anything like the anecdote below.
I remember in the mid 1970's an acquaintance was doing a virtually unlimited budget restoration of a 67 Corvette. Before the car was even painted, it was at the body restoration/primer stage, he paid $1500 just to have the hood exactly match the nose. Using Google's inflation calculator, $1500 in 1975 is the equivalent of $6,976 today. Best I can remember, not only did the hood exactly match the front clip, the space between the hood and front clip was something like 1/16 inch.
My sympathy for being at the stage where you've painted the car and now have this gross hood mismatch problem. Seems like the body shop should have been ahead of the ball on this one.
One reason for being very sympathetic, is that astoundingly, I'm at this 68 juncture again!! My 70 Coupe is also a Bondo masterpiece. When I bought it 20 years ago, I just didn't inspect the car that closely. The hood did fit however. When I peeled the onion a few years ago to restore the car, I found that the front clip has been horribly repaired with Bondo and crude fiberglass work. When I removed the radiator bracket, the right side of the front end collapsed and basically cracked in-two!
To do the job correctly, I'm going to have to replace the entire front clip with repro fiberglass. The OEM stuff is no longer available I've been told.