Post pics, we need to see what you are seeing, it does sound like the unibody and or hood are not in their proper shape.
I would try to get the hood sitting flush with cowl and fenders and then start working on the hinges, there's lots of tweaking that can be done to the hinges and because some of these hinges are quite worn you may have to enlarge to mounting holes so the hinge unit can sit farther down than normally.
Also the 8 hex head screws that hold the fender on in the gap between the fender and hood are not a standard M6x1mm, The head is not as tall/thick as the rest of the M6x1mm screws and there is only one thin washer with no lock washer.