As far as I know, the A/F ratio is specified in the base fuel maps, which are set lean by the factory. To these base fuel maps corrections are applied to compensate for engine temp, engine & sensor wear, battery voltage etc... from the tuning guide I linked to earlier:
5.1.2.5 Exhaust Gas Oxygen Measurement Corrections
The EGO and AFV are corrections which are derived from the measurement of oxygen in the exhaust, using the O2 or Lambda sensor. The corrections are derived and applied to compensate for other uncertainties, such as changes in air pressure, engine to engine variations, air filter clogging, exhaust deterioration, engine deterioration and sensor calibration errors.
The EGO is a correction derived and applied during Closed Loop and Closed Loop Learn control regimes.
The AFV is a correction derived in the Closed Loop Learn (and Open Loop Learn) regime(s) and is applied in the Open Loop and Open Loop WOT control regimes.
For Buell X1, S3 and XB engines before 2010 model year, the O2 sensor is installed into the rear header only, this is the input to the ECM to calculate the EGO correction. Although the front cylinder's mixture is not monitored by the ECM, EGO and AFV corrections are applied to both cylinders in the same manner.
More advanced EFI systems use additional measurements to improve the accuracy of the air flow calculations. For further reading, see reference 9.
Here is a link to a quick start guide by xoptiinside which outlines the basic steps to follow when tuning your ecm:
http://xoptiinside.com/yahoo_site_admin/assets/docs/Is_tuning_your_bike_a_little_blurry.24475730.pdf
But first:
set static timing
clean throttle body
set tps
clean plugs
check plug gaps ngk plugs standard plugs
set gap to .035
clean air filter (high flow )
reroute the breather tubes
start tuning now
dont skip the step order
Good luck