The  red line is correct stagger and the light blue line is with the stagger that Yamaha supplied the bike with.

To diagnose, use your EC997  Eddy Current Dynamometer and integrated 4 Gas EGA to inspect overall CO% numbers for roughly correct numbers and then, inspect residual O2% for excessive values. If the CO% is good, but the O2% is high, then the stagger is absolutely incorrect and needs to be addressed for best power.

Bikes that have incorrect stagger will often pass through a dyno test on an inertia dyno without a hitch or a hiccup. Even with an "air fuel ratio" sensor (a simple, very expensive O2 sensor with increased range that extends up to places where the engine doesn't even run) attached, the average reading of only one gas (residual oxygen) still looks just peachy on an inertia dyno. Send the guy away - you think you did a great job - you just aren't sure why his bike seems low on power as compared to others. Maybe it's the pipe? It's the weather, yep, that's it...
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To properly diagnose incorrect stagger, you need to do Step Tests with the 4 Gas EGA EC997.

You NEED the 4 Gases.