You're on the right track for sure (and x1000% on the S1000R) testing the O2 is as simple as watching (or datalogging) the output voltage to know if it's giving the ECM the right signal for closed loop operation. ECMDroid is a powerful and easy tool to use for diagnosis.
Your AFV should stay at or near 100. If it's changing drastically, you have a problem. AFV is a global map change, I think it's a rudimentary ham-handed way to do it, but thats that cards were were dealt with both DDFI-2 ('03-'07) and DDFI-3 ('08-'10).
I would shy away from changing any mapping yet. First fix the bike, then modify the bike. You're looking for trouble otherwise. I'm not aware of any "newer, stock tune", but I would recommend the 'race tune' (even the one for a stock muffler). It is a big increase in rideability and power, but resist and only do it after you get your bike sorted.
IMO