Without an A/F ratio chart we can't see how rich it is to see if it's a problem. You'd usually want it to lean out a bit towards the top, but not so much that it will cause trouble. I was thinking possible air flow issues from having a restrictive air filter or such, but 2112's secondary throttle body valves seems a better explanation. They are there to restrict the air flow in certain conditions, most notably in 5th and 6th gear to restrict top speed. Removing them wouldn't require any other adjustments.
One thing I'm wondering is why they zeroed your ECU and how it then looked fine on a dyno except at high speed in the top 2 gears. Usually the Vee has a very lean spot around 3500 rpm, did they not see that?