ok, i dont know a whole lot about 4 stroke engines, im a snowmachine guy( snowmachines are 2 strokes, and are carbureted so they dont have the EFI jetting etc..) but, from what i know, when you put an aftermarket intake and exhaust, it opens the engine up to be able to breathe a lot easier, same concept with a snowmachine, when you allow the engine to breathe like this, it always allows the bike to run more lean, when you run too lean on a snowmachine you take a chance at cracking your postons, dont know if its the same on a 4 stroke but i cant imagine its much different, either way, you never want to run someting too lean.
if you add the full pipe and new intake your going to run lean and i would really suggest you get the pc. yes you will notice a lot of gains after adding all that, and your bike will run like a bat out of hell for about an hour if its really lean, then it will most likely blow something. the pc will richen her up and run it at a normal feul intake area and im pretty sure the pc adds a little horseys as well.
Hopefully other people like scuzz post on here to cus im not the most knowledgeable when it cmes to 4 strokes and quads but i tried to help.