When I picked up my boat last year with a 2001 6.2L it had that issue, with a new IAC valve the problem was solved immediately and no issuses since. I am curious about the trick with the little foam piece though.

I have the foam muffler in my throttle body (496). I've replaced it once as it was looking dirty. 325 hours on the original IAC so not sure the foam is a problem as long as it doesn't plug up. I carry a spare IAC valve as I know I am on borrowed time. I'm afraid to change the original out as it has lasted 3 times longer than most. The new one probably will shoot craps after 100 hours!

One thing I am curious about: this engine has also been running richer than the other. More soot on the transom. I imagine the tune up will help. Does the IAC help this or is there another thing going on?

if the IAC is not working properly, it could be causing a rich condition at idle and therefore the soot.

IAC first if it does not clear up and still runs rich try to have the motor scanned to see how the MAP sensor specs out. MAP sensor might be the problem of the rich condition if IAC does not clear it up.