the center hood opening on my 1957 TO-35 shuts good now, but it still rattles sometimes.
I keep a piece of soft rubber mat under it to slow the rattle down some, have to move it around from time to time.
i have has to reweld the main supports on the hood once or twice over the years.
you might check them, these are the pieces that are part of the main hood, that go across under the small flip up hood. They are under a lot of vibration pressure and will break, that may be why you small flip hood is not level with the main hood when its shut.
mine looks good per fit, but it still rattles some. i have just learned to live with it.
when they put the screw down on the next generation hood it was a major improvement.