I purchased a 04 F4i last November with a full Yoshi header back exhaust, K&N, and Power Commander iii USB.

The end of the Yoshi muffler is turning a very slight blue, I decided to see what map he had loaded in there, turns out that its a map for 01 completely stock bike, I did find another map from their site.

Pic of the exhaust:

 

A local dealer wants $30 for 3 dyno runs, and $200 for a tune. Im going to try a richer map, will also be taking it in for a custom tune (if they know what they are doing...)

 

Only go to a dynojet programmer. They will have the software that interacts with the PCIII and does the automatic tuning.

Just remember, you're not going to gain a lot, maybe 3-4, but it will be much smother.