Gary, I've done the way you're talking about. I rented a dyno for an hour and did about 12 pulls, adjusting the Tuneboy tune each time. It was fun as hell, informative, and provided me with a better tune than the original tune I had.
There is a way to hook up Tuneboy to a dyno, but I just don't know the details, which is why I pay a tuner to do it.
Only advice I can offer when doing the tuning the way you're talking about is to familiarize yourself with the fuel trim feature. Also, don't get caught up with that A/F table - just leave it alone because it's nothing more than another f-table. Also, remember that any trims taking place at 0.0 will affect the entire L-table. And one last thing that I picked up from looking at Tuneboy maps from other bikes: to reduce decel popping, make the F-values in 1.0 equivalent to the f-values in 0.0. Another way to address that decel popping is something dougl taught me - add some fuel to the 0 values of the L-tables.