I've used dynos twice for a Manx Norton. Each time (different dynos) the operator suggested I accelerate up to speed in top. Maybe Japanese bikes can do this, but old Brit ones can't. Use the gearbox to accelerate the dyno roller up to speed before doing "roll-on's" in top or maybe third.
Ideally you want to look for a dyno used to race bikes. Many dealer dynos are used merely to sell performance equipment. "Your GSX-R whatever is under power, buy these race cans at £700 and a miracle will occur, requiring only money, no tuning skill required."
I set the ignition first - easy to alter because it is belt driven via a vernier - by first retarding a degree at a time then if it wasn't improving, advancing. Then I set the fueling, which again is easy, this time because i use a Gardner, and mixture through the usable range is controlled by a single click-stop needle. Presumably you'll have to alter needles, slides, jets etc. Time consuming! I'd be inclined to sort out the main jet, then fix the rest by traditional suck it and see methods.
FWIW, I have been told that the exhaust gas analyser OUGHT to be in the pipe that you are setting for, i.e. rear or front, but that in fact the reading doesn't alter much if the sensor is placed downstream of the point where the pipes join. If true this would be good, because getting the sensor in to the pipe from the rear head might be a bit of a struggle. Best of all is welding bosses to each pipe to allow a lamda sensor to be fitted to each in turn, because then you don't have to negotiate the silencer to get to where you want the sensor to be.
I haven't bothered with the Vin. It goes OK the way it is (an easy 100 mph when I get the red mist) and the plugs look OK - which for modern fuels is less "light brown" than "off-white". A bit of grey in the silencer tailpipe is a good sign too. Magneto, 34 deg BTDC, 7.3, NGK B6, original carbs (Shadow), Robinson cams, 180 main jets, cooking unleaded, all other settings pretty well by the book.