Good that you are finding these things, but most of the guys tuning have long since resolved the secondaries by either removing them or keeping them 100% open via ECU control.
The triple intakes/ram-air/piper-cross etc are proven to make power. Not like import cars, or hardleys, or even most K&N drop in filters, they do work on the R3 and there are dyno on the forums to prove it, so it's money well spent.
As far as the exhaust lenght/diameter/collector type etc, I have long since given up doing the math and mental antics myself, and have simply watched what people are producing. From the dynos available you will find there is a set that exists to cover all bases. You can get huge low end torque with a certian brand, a good balance of low end torque and top end hp, or an anemic bottom with crazy top end with another company. They are all out there already, just take some time to peruse the forums here.