Small road report from this morning's ride into work.
I haven't touched or tweaked the Power Commander at all. No calibration, no nothing, so take this all with a grain of salt.
Upon first riding the bike this morning, I found I had less power around the 5K range, but it would come back on after 6 or so. After riding for about 5 minutes, it seemed to remedy itself. So there's something there with a cold engine, at least in its uncalibrated form. I plan to get it calibrated in another week or two.
As for the quick shifter, I experienced one time of probably me not pressing hard enough and ending up in neutral going from first to second. I also had one or two instances of me kicking down (I'm in GP-shift here now) and the bike not shifting, so I had to kick again harder and it went. I was at about 7K when this happened. This all happened during the first half of my ride, the rest seemed to be OK. So take what you will from all of this. There's definitely some of my getting used to this shifter (especially compared to the one on my S1KRR), so right now I'm taking this as pilot error and not the quick-shifter's fault. We'll see how it goes on the ride home later.
I've been taking the twisty way into work and back the last couple of weeks to try to get some revs and some miles on the engine. I seriously think I enjoy riding the R3 more than the S1KRR on those roads. Less drama, more fun.