I tune bikes on the side to help pay for my racing habit and have been doing such for many years.
I tell you some secrets that I have found out, some recently.
1) Bikes with extremely high efficient head flow, have more of a tolerance with the tune. In other words, they make almost the same power running on the slightly rich side as they do "dead on". While I haven't put my S1Krr on my dyno yet, I am sure it would fall in that category (darn 600 mile limiter). My Hayabusa with a "uber-dollar" head, makes 207.5 wHP on pump gas at 13.1:1 AFR, it makes 204 wHP at 12:1 AFR.
2) While it is true that most bikes built in the past 10 years have enough sensors to adjust properly for atmospheric conditions, they do so based on a programming assumption of a stock engine. Once you modify, in anyway, the stock setup, the atmospheric adjustments become less and less accurate as you modify further away from stock. That is why I rather "burn the ECUs" than use a Power Commander when possible. I have more control that way.
3) In all due respect for the Power Commander folks, their off the shelf maps typically are on the rich side of things AND while close, the shape of the maps are sometimes questionable. However, given that they have to setup the maps for the "masses", including knuckle heads that run crappy fuel, they overall do a good job. But, tuning on a dyno has definite advantages even with an autotuner. Even if your autotuner is “dead on”, it would wise to just check it on a dyno. (more worried about 100% throttle than anything else).
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