"This may sound like an insanely crazy "farmer fix" idea, but would it be a viable option to carefully use a belt sander to gradually touch up the ports until all made contact? Just a thought I brainstormed right now."
I'd try two gaskets before trying the "farmer fix" (we'd have called it a "cob job", instead of insulting a farmer)

"Also, if the manifold must be surfaced professionally, would that not make the rings in the intake ports stick out too much so the rings themselves prevent the manifold from snugging down on the head?"
You are correct - that is a distinct possibility (and, it is perceptive of you to recognize this potential problem). You would have to grind-down the width of the rings.

Those are why I go to two gaskets, first. Are you using the very nice, but expensive, one-piece gasket? If you are, you might find the cost of a machine shop work is less expensive than the cost of two of those nice gaskets?