I used the woolich software when I flashed my 14. This was done on the dyno. Fuel adjustments where made during this process and flashed directly into the ecu. No PCV.
If you just removed the restrictions and raised the rev limit, opened secondary butterflies,etc,
Then a run on the dyno WITH a PCV would be needed to make sure afr is good.
Usually flashing the ECU is to remove restrictions, my mechanic instantly gave me 10 more horsepower he said then he bumped up the rev limiter to 11,300 RPM's, removed the top speed governor, and changed the timing restrictions throughout each gear and made my fans come on sooner.
As far as any mapping goes, I am using "Rapid Bike" by Demsport which is one of the best auto tuners on the market, I also got the "My Tuning" module and O2 sensor in my Brock's mid pipe. I sold my PCV but it was fine for the most part. Using a power commander is easier for a dyno tuner to make adjustments for you as not everyone has the tools or know how to work with our ECU's.