I had a Power Commander 3, Staintune pipe and K&N filters on my 2005.
I clean and oil the K&N filters so that they work properly, I love the sound of the open pipe, and I ditched the Power Commander.
Ditching the Power Commander was the best thing ever - it is much better to ride without it. The low rpm torque was great with the PC but everything else was terrible.
I have the Power Commander and Akraprovic on a 2007 K1200R Sport... took the max power from 135 to 149 and torque from 78 to 86. It got a little lumpier, but nothing worrying .... remained nicely rideable.
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