Again, to be clear, a Power Commander (or any other fuel injection controller) is not strictly about horsepower. It is one factor, and one that a lot of folks look at first, but really only one. A Power Commander helps to tune the fuel injection, with the goal being a smooth and even Air/Fuel ratio from idle to redline. No one can argue that the stock ECU mapping is lean in some areas, and rich in others - with the stock exhaust, slip ons, or a full system. These rich and lean spots affect driveability and throttle response. Some folks are VERY sensitive to these changes, other folks are not. In general though, one ride on a properly mapped bike with a Power Commander will be enough to convince most folks. If you have not been impressed so far, perhaps the mapping/tuning was not done well or carefully, perhaps there is something else affecting things, etc. The side benefit of a clean Air/Fuel ratio is increased power.
Look at it this way. Your motor is a big, glorified hot air pump. Bone stock, the air goes in and gets pumped out in specific known volumes. This is why the size and shape of the airbox and intakes and filter are so important. They are "tuned" to help produce smooth clean crisp power. The same holds true for the exhaust. Once you make a change to the exhaust, in general, you are getting more flow through the motor. More air without fuel at some RPM's, and perhaps less air at others (rich) because of resonances etc. You have disturbed the status quo. A Power Commander brings the orchestra back into harmony - restores order to the universe, etc. Restores the status quo - at a new flow level to compensate for the exhaust.
I cannot directly answer questions about the PCV and pre-2009 models right now. I hope you understand