Ok, so like I was saying, if you had found crud in the coolant, it could have found its way to the intake.
Since you report that the coolant is clean, then a leak of some kind into the coolant isn't likely.
If the manifold passes a pressure test, then I doubt there is a problem with the intake.
I don't know the history of this issue, or how long its been apart, was the intake new or used when you got it, etc... but if it is running fine, the plugs look good, and you're not "using" coolant, chances are that its just some light duty crud that has settled into the intake. Possibly its just some rusty film? If that passage has a couple steel plugs in it from when it was made (to plug the sand core supports for example), then maybe they are rusting, and because it was sitting awhile, perhaps it has tainted the water that was sitting in there? Just a thought. I guess I'm out of ideas at this point...
