A machine shop where I worked part time had a BIG belt sander- - - -like 12" wide and over 3 feet long. We would use it to clean up manifold flanges like that. It would also be possible to set it up on a mill like a Blockmaster and machine the pits away. As long as there's a little bit of the flange standing proud of the manifold runners, you'll be good to go.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
Cringe and wail in fear, Eloi- - - - -we Morlocks are on the hunt!
There is nothing noble in being superior to your fellow man; true nobility is being superior to your former self. - Ernest Hemingway
Love your enemies and drive 'em nuts!