Devious2XS @ www.triumphrat.net:
You set up the TuneBoy to emmulate a PCIII.
Then connect the dyno pc to your laptop running TuneBoy via a spare USB jack on laptop.
Make a pull on the dyno (at a given throttle position) and a Dynojet will calculate trims to adjust the cells at this throttle position. You can alter cells manually, or simply click a button and the corrections will be made for you. Save each change in the map under a new name, so you can go back if the change actually makes LESS power.
Make another series of pulls at the same throttle position, and if no corrections are recommended, you are done with this throttle position. Generally several pulls will be required.
Change throttle position and make another pulls/adjustments until all load/rpm cells are corrected as required (mapped).
Now, IF you change ignition timing (which a PCIII will not do), you need to check air/fuel ratio again.
Air/Fuel ratio (AFR) will trail rpm by a good bit. This can be several hundred rpm to 1500 rpm - depending on the acceleration of the bike on the dyno. This is because the O2 sensor sees gasses later and responds slower than the engine can rev.
Note: This is ONLY tuning to AFR, many times more power can be had at various rpm points than just targeting a given AFR. Multi-gas analysis can help in this.
Also, the load on a dyno may not be the same as the actual road load, and some on-the-road tuning can help get everything "just right".
A lot of tech BS, but I hope it helps.