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

Compare the "almost clogged" cooling passages against your head gasket. It could be that the clogged ones are not passages at all, but purposely blocked off by the head gasket. If so, the build-up is normal. Your other coolant passages look normal, so don't slam the "5K since rebuild" guy yet.

I made that mistake in my dumF kid days when re-assembling my slant six and I found two ports didn't have a matching hole in the head gasket. For some stupid reason I decided to drill a hole to match. Started up and it started over-heating. I decided those holes were supposed to be blocked and were only there as part of the sand-casting process. Since everything was new, I was able to lift the head with the manifolds on and slide a new head gasket in place and the car ran fine for years after.

Too bad you didn't do a compression test before removing the heads. That would have told you if you need a ring job too, which can be done with the block in the car on many cars.