My experience and what i think i know.
(I ran my bike stock for the first year)
Bike ran very hot because of the lean AFR from the factory to comply with EPA emissions.
Wanting a little more grunt, i put on slip and did nothing else until i could afford the pieces i wanted. Bike ran the same as stock.
I got a Ness Sucker AC, and still ran the stock exhaust.
bike still ran hot and lean
When i got a new full exhaust, i also purchased a Power Commander V, with a downloaded map from Fuel Moto. Bike ran ok, but still hot because i did not have it dyno tuned, and was just a downloaded map from a dyno done on someone elses bike with similar AC and exhaust set up.
I changed maps a few times until i could be somewhat satisfied.
i recently added cams and a 107 kit, and had it dyno tuned. Bike has never ran better.
moral of my story is, a good Dyno tune is the only way to go if you want your bike to run good, and in order to Dyno tune your bike, you need a tuner to be able to modify the ECM. if you change exhaust and Air Cleaner, your bike will get you down the road just fine. But it wont run good. They dont run good stock from the factory.
Here's some more reading for ya: