What I want to do is take the power from the high range and transfer it to the lower and medium range where I will be using the bike a lot. Using this rapid electronics kit I expect to achieve that.
I'll be watching with some curiosity what you are able to achieve. You might consider a cam change, and/or some adjustable cam timing gears. The valve overlap is pretty narrow on these motors, hence the moniker - Testastretta 11°. The narrow overlap angle increases low-mid range torque (and subsequently, HP) at the cost of top end performance. I think the inherent limitations of the engine design is going to hold you back and you're going to run out of additional power with the electronics pretty quickly. Hopefully you prove me wrong.
Wish I could but am not smart enough. What I can offer is my observations of the PCV control panel while running it on my 1100evo. A 13.2 AFR was recommended as a starting point. Once entered in all map fields, I then observed the injector data from both cylinders. The injectors were operating differently. This meant that to maintain the selected AFR the injectors pulse commands were different. Also, using the AutoTune, the trim tables were always different for each cylinder after a ride.
Correct me if I'm wrong, but on the air cooled bikes the rear cylinder ran a bit hotter than the front due to restricted airflow, even on the unfaired Monsters, Hypers and Supersport CR's. It's pretty common to set belt tension looser on the rear as there was some anecdotal evidence that the extra heat was increasing belt tension and people were seeing more belt wear on the rear than the front. Airflow isn't a limiter on a water cooled bike, and I admit to this being my first water cooled Ducati, but I was looking at the cooling circuit and it seems that cooling is done serially, not in parallel, so the water goes from the pump > radiator > front cylinder > rear cylinder > pump. Is Ducati keeping the rear cylinder warmer because it's what they've always known how to manage all along?
It's common for the plugs to look different front/rear on the air cooled carb'd bikes for this reason, and I suspect this extra heat is also what's being auto-tuned for.