I'm at that point (Head job vs New Motor)

There's a perfect reason for the blocked coolant passages. The headgasket is in the way!
Maybe nothing is harmed, but with 1000's of miles... I'd be saying check deck flatness, and if that's okay try a new set of gaskets that don't block any coolant passages.
That gasket isn't blocked, it's corroded from the coolant trying to get to where it's supposed to be.

And everything is going to be fine! PM me for moral support and free parts