Quoting fivestardsm:
First off, is it an OEM hood? If so, you might not need to align the hood, but the fenders. If you look at the line where the fender meets the A pillar, they should be even on both sides. Also check at the door/fender corner.
If it is the fenders that are slightly out, it is easy to just loosen the top bolts and move them around a little bit. If the fenders look to be completly straight and aligned to the doors, then you can "pry" the hood over to the larger gap side with a piece of wood. Use a 1X2 or such or something that is Mallable just so you dont chip the paint. You can also put a shop towel between it and the hood to protect the paint.
I would try these few steps before I reeamed out the holes.
excellent post!
You can measure the engine compartment with a trammel bar to verify the alignment of the opening and fender attachment points. It may be a combination of factors. Trying to use one surface as a referernce only works if that surface is accurate and true to the centerline of the car.
If the heighth at the rear looks funky, the factory had shims under the top rear fender mount on almost all the cars I've ever had apart. Many times, those get lost when the sheetmetal is removed, and the original alignment is lost. This can lead to all kinds of funky gaps and mismatches in the alignment of the front body panels, and make it hard to nail the fender/hood gap evenly.
Good luck, and post a pic of the problem.
We've got a couple of body techs onboard here, and they might have some ideas if they can see how it looks. to start