I'm not up on modern tech, storage of info, etc, I only know about discs and sticks. ....But I do know a bit about tuning, and if you used my map on your bike, with the changes you state, it would run like a five legged dog.
The point I'm trying to get across, after reading your understanding of the subject, is it is important that people are familiar with how the power comander works, how correct fueling is imperative for longevity of the bike, and how it runs, in relation to modifications to the bike.
The best base or start map for your bike with just an end can is the stock map, or one of those provided by dynojet that corelates to your setup.
Once installed on the bike, the power comander will stay there, it does not program the ecu, the ecu is locked.
It is fun squeezing a little more zip from bikes, or any other mods we get up to, but many are made worse by people medling without knowing where they are going with it. Bit like me and computers......that's where dyno time pays off.