Have any body panels been replaced, such as quarter panels?
Non-stock panels, if not installed correctly can really throw you off on panel fitment.
As for body alignment, I always start with the doors, align the rear of the door with the rear quarter and body line, while you are at it check for door hinge sagging. Next move to front fenders, front door gap and then the hood.
Remember hood bumpers and weather striping can affect alignment as well. After you get the gaps set then you can use a straight edge to start body work.
As others have stated, time and patience is what it takes to get them right. Also remember these cars never had that great of body gaps from the factory. I wish I was close to you so I could help.