Well there you go. Sounds like the 06 manual is more complete than the 07 manual or else they later got concerned about the tube protrusion distance past the top tree, which I trully believe a star nut movement would be to small to matter.
I didn't do the fall away test as it seems absurd to me especially giving you that big of a tolerance for everything to be O.K. I have never had the steering stem apart on a street bike but did it sevral times on dirt bikes. I adjusted mine like I did on dirt bikes which was hand tight then a couple taps with a rubber mallet and drift. I think it's just a bit tight, when I'm going slow it kinda feels wobbly probably because the bars don't move quite as freely as before but my neck bearings aren't taking a beating either because they are to loose.
Well I wouldn't call the TEST absurd. If you ever have high speed wobble you probably won't either. I test mine every year or so. It don't take long.
First raise the front end (or bike) off ground on a near level surface.
Then remove the clutch cable (use right size snap ring pliers or you will loose the ring). Kinda greasy mess but necessary.
Put a chair in front of the front tire, lay a pencil or any such object on the chair and lay a weight on it (5 lbs or so) to keep it from moving.
Test your fall away first just to find where the center is, (rarely will it be with the tire straight ahead). Once you locate the center of fall away, slide the pencil and weight to the center of the tire while it's sitting at said center of fall away.
Then tap the tire one way and note the distance it moves until it falls away. (I use a measure tape)
Then tap the tire the other way and note that distance. The total of both distances should not be over 4".