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 First, verify that your hood hinges are correct. Make sure your rubber body mount cushions to the frame have not broken down over time. Replace if needed. Good start. Next, verify that your frame is straight. Get the measurements from a manual, and cross measure the points to be sure the frame isn't bent or twisted. If you can't get the measurements, pick equal points on both sides of the frame, like matching bolt holes, to use for measurement points. Next, with the hood off, loosen all fender bolts and align the 90 degree corner of the fender to the cowl vent panel and windshield valance, on each side. Shim to get perfect height and align for about 3/16 space between panels. Snug up the closest bolt to keep the alignment. Then cross measure from rear on right to front on left fender and repeat in the other direction, making an "X" across the nose. If square it will be equal. Move the fronts of the fenders to square the nose. There should be adjustment on the core support, and from the core support to the frame. If you think you have to slot a bolt hole to make it line up, something is bent. Find out what it is before you proceed. Measure across the back and front for width, and compare to the hood. You should have equal spacing on both sides. Then look at door gaps. If they are not equal, and parallel, shim the front of the fender for height to achieve parallel door gap, and tighten bolts. Re-check all previous measurements to see that nothing has changed. At this point if your doors gaps are equal and parallel, but the fenders are out further than the doors, you may need shims between the bottom bolt and the cowl to pull the bow out of the fenders. However, if they stick out from the doors, and the curve of the body lines is exactly the same, you may need to move the hinges out. But, if you have to do that and your weatherstrips are old, you will get wind noise. You may have to live with the fender to door surface misalignment. Remember, these bodies were not built to the tolerances of today's cars. When you are ready to put the hood on, put a couple of layers of masking tape on the fender edges so you don't scrape the paint, and close to hood very gently to check alignment. Some people remove the hood striker when doing this so the hood won't latch while adjusting. Remember, when you do this, the body lines have to match. If they don't, on an old car, it is very likely that he body mounts have sagged and need to be replaced. All this is better done as a two man job, if you have help available. Good luck.  

Note:
You may need to get it square by loosening the front radiator support mounts and moving it it to center. The core support should be centered in a perfect world, but if your front frame is a little bit off, to line up the sheet metal to the body you may have to move it slightly off center to make that happen.

Thanks to:  Chris Ferrante