I *think* that what Scott was trying to show is that the way of setting them at the factory is plate levels AND actual vacuum, re: customizing the bikes fuel map(s). I read that post, and it was emphasizing that the map is made assuming that the flow through each butterfly plate is the same.
But, that doesn't mean they don't set the plates all at the same spot. Doesn't mean you shouldn't set the plates at the same spot. In fact, just the opposite, for them to assume equal air flow through each one (within a tolerance), they have to make sure they are all set to open the same amount. Whether at idle, 20%, 95%, whatever.
That's why I like the fluid idea. I bet Yamaha made sure each butterfly allowed the same amount of air through when closed, and the fluid method let's you do the same thing. They had it off the bike, check, set, paint. You can do it on the bike, like Randy said, one on each side will do since it's set up *2>adjustment>2* plates. I mean, no reason to complicate it any more. If you want it close, most likely as close as any garage would get it, well sounds like you're about there. If you want to get it exact, since you're already into it this far, do the fluid. Doesn't take long. Oh, and by feeler guage, pretty sure he meant at any given small opening, you can match them, using feeler guages from edge of plate to inside of TB.
But either way, that's just my technical side. My riding side says good for you on listening to ALL of the opinions, and getting it damn close. You didn't just run the bike all over potentially damaging something, but instead asked and adjusted and asked again....and your bike running close to what it's supposed to be. Now it's up to you whether you want to get it *perfect*, and you're armed with all the knowledge you need to do it, and the sync afterwards.
Nice job Steve!
Loren