After all the trouble I had with the Fuel Nanny I decided I'd give this a try and hope for better results.  The fuel nanny is the low tech attempt at what the power commander does.  Off the bat the bike felt better, and wasn't stalling....so I was happy enough.  You can use a laptop to load different fuel maps so I grabbed a few, and started testing them out.  It was pretty neat taking the bike out after each map was loaded because you could feel the difference.  Some had more low end, some had more top.....some just sucked across the board.  Hopefully next year I'll get the bike down to a Dyno that has the software to program the Power Commander III.  All you do is take it to the dyno, they hook up the computer and you make a few runs.  Each run the computer will adjust the mapping and in the end you get a custom map made specially for your bike.  It's just alittle expensive so I haven't done that yet.

UPDATE: I did get the bike to a Dyno to be tuned, but they didn't do a very good job.  No software used, did it all by hand.  Bike ran great....as long as you had the throttle wide open, rest of the time it was bogging down.  Good waste of money there.  If you do go to get it tuned, make sure they have the right setup from powercommander, I think it's called "power link".  Otherwise you could end up with some crappy mapping like I did and pay out the nose for it.

The powercommander software in use.  Just hook up a laptop and tweak away!