The driver’s side is pretty solid/straight on but the alignment of the two on the passenger’s side has always bothered me. I had always thought about trying to adjust the hood until someone mentioned it to me it is really the Front Fender Extension that is throwing it off more…DUH! You can see in the pics that it needs to be raised slightly where it meets the hood and the gap will close significantly. Have not really looked at it in detail yet but is there much to loosening it and re-positioning?
If it were loose ( and that’s what caused it to ‘sag’ in the first place ) then gently yanking on it ( upwards ) will probably work, for a time. But after awhile, with vibrations, it will resume it’s old position - probably where the threaded studs on the extension are resting on the bottom of the holes in the front radiator support.
I would remove the inner / front splash shield and using a socket with extension ( and your lucky its the passenger side - no vacuum reservoir in the way ! ) , loosen the hex flange nuts that fasten the extension to the rad support, reposition the extension, and tighten. A much better, more permanent fix.
Hitting the soft pot metal ( even with a wooden block ) could more than likely wrinkle or dent it.
If you notice that the fasteners indicated for attaching the extension to the fender are a #10 lock washer ( 34803-S ) and a regular 1/4-20 hex nut ( 33795-S ) but that has not been my experience - what was used was a flange nut.
Yes its ok to adjust the position of the extension, just not ok to try to bend the edge of it. You are right, they often weren’t aligned very well from the factory.