The Power Commander is a great tuner.
They have maps up on their web site for your configuration.
I would look at the map they have and see what is different from your map.
As far as more air is concerned, if you don't already have one, get a K&N air filter.
From what you have mentioned, I suspect you need to add fuel in that rough spot-- 2% initially in the cell just before the lean condition and through it. Then go for a ride. If it has changed, then you are moving in the right direction.
You have a great exhaust so I wouldn't change it. Once you have the performance issue resolved, there are blue removers that will make it look much better.
If you are still hungry for power, you can get some cams and a larger throttlebody. From there is big bore, stroker and turbos. It's just money.