In my limited experience I have found that there is several different styles to achieve a common result. In my opinion, I like tuning with the factory NBO2s' for drivability. Also know this, don't keep yourself in a box with a specific rpm range. It's more important to prioritize load over rpm in most situations like you are dealing with. For example: You may not have PE coming in until 2500 rpm, yet you are climbing a steep hill, under heavy load, (85 kpa) at 2200 rpm, your not gonna want to be at stoich or leaner. In that scenario, your gonna want to shoot for something in between full PE and stoich, say .9 or 13.2 afr. The exact opposite scenario would be, you just pulled it into 3rd gear coming down a hill, very light load (45 kpa), 3800 rpm in preparation of going into PE but you never did it. (never smashed on the loud pedal) During that light load scenario, if you tuned the VE mostly based on rpm you would be dumping significantly more fuel into the cylinder than what is desirable.
You may be interested in reading a tuning book from someone like Greg Banish if you need help understanding the basic wants/needs of the engine and how all the systems work together, effect they have on each other, and how to get them to work as a team for your common goal.
As Alvin mentioned, if your reporting the wrong data, your gonna be chasing your tail. That's another reason I like to start by prioritizing the factory NBO2s' and use the LTFT/STFT to get things in the ball park if possible on a street car.
I'm still struggling with the fact that I can make mine feel better in OL, but I leave it in CL with the LTFT locked down to plus 1 percent and minus 10 percent because I don't have enough experience to know what's gonna happen when the weather does a 180 on me or the baro changes by 20 percent during a drive it it's in OL.
I came from limited experience tuning stand alone PCMs from the likes of Holley and Fuel Tech. Having CL control with a WBO2 is a slightly different animal.