The AD Front Clip Alignment Procedure to which Jethro refers can be found near the top of the first page of this Paint and Body forum under Tech Tips.
If I were you, I would stop until you can install the proper shoulder bolt for the hinge. If your remaining bolts are showing signs of wear, you'll want replace them as well. There are just too many tails to chase aligning a hood to take a chance on worn hinge bolts.
The number one thing to understand is that the hood adjustment comes first. That procedure has nothing to do with adjusting the fenders.
You set the hood up in perfect alignment with the cowl, and never touch it again. I cannot stress that enough.
You then adjust the fenders until they align with the hood.
