Hey PowerCell, sounds like you have been around the block a few times working with the ECU software. I wonder if you know anything about the secondary butterflies setting. I have read posts from folks who have removed these altogether in an effort to cure this or that problem - this just seems like a bodge to me.
I can see the secondaries acting like the slide in a CV carb in order to keep the air velocity in the throat of the throttle body high. On my bike with a stock map, it feels decidedly as though the secondaries open late, causing a big hesitation. Noise abatement? I have to imagine that the "open" map clears this up, based on what others have written, but I won't know until I try it. I guess you could map all of the secondary settings to 100% in order to keep them open and achieve the same effect as removing them. This also seems kinda like a bodge, the exact same bodge, actually.
Then again, there are plenty of EFI bikes with only one set of user-controlled butterflies that run great. Maybe the secondaries are all about emissions?
Anyway, where I'm going with this is your experience with creating maps on a dyno (or watching someone do it, whichever)...seems like the dyno is typically used to find A/F ratios at WOT to correct for open pipes, etc. Great, but I wonder if your dyno guy is also able to tune at part throttle openings and low to mid RPM, which is in my opinion where the 990 needs all the help. Refining that part of the map would be huge.