The Power Commander is the way to go, if you are going to make more changes than just intake, and exhaust, ie, internal motor work.
With the Power Commander, you have easy, and precise adjustment, that's almost infinite.
The Cobra has a crude, less fine adjustment.
The difference for the changes you plan would be slight. The Power Commander might, emphasis on "might", get you a tenth of a second quicker 1/4 mile time.
Keep in mind, the Power Commander is only going to be at it's best, after you have the bike dyno tuned. Having the bike dynoed, will cost anywhere from $100, to $300