Your A/f at light load, cruising should be high 12's low 13's. As long as you are seeing low 12's or high 11's WOT. You are good. If you want to do yourself a favor, look into Schyco Sled's Bridge for the Nytro with super or Turbo. I installed it and this is the first time I have been totally happy when riding at all elevations and temps.
As for any specific setting for the GEMS, read up on the functions and what setting does what, because it changes daily! Due to temp's, barometer, etc.... with the Bridge system, just ride!