Its not the jet kit that makes the real difference, per say, but whenever you make adjustments to the way the engine breathes, you need to make adjustments to the fuel/air ratio at the same time.
Lets say you take a perfectly stock motor, and the jetting is set up perfectly for the airflow. If you make a change, say K&N filter pods, and a full exhaust replacement (old was 4-2, new is 4-1), and both are capable of flowing a considerable amount of air than the stock setup, the engine is now running on the lean side. More air plus same fuel = higher air/fuel ratio.
If the air/fuel ratio is to high, first off, the power just won't be there. Second, since there is more air in the combustion chamber, the temps will rise, and the possibility pre-detonation might occur increases. If there is alot of excessive pre-detonation, damage in the combustion chamber can occur. If you're lucky, its just a hole burnt into a piston.
So what you would do to bring the air/fuel ratio back to an acceptable level would be to increase the size of the main jets in the carbs. How many sizes it needs to be increased can only be determined by changing and testing, over and over. I always recommend going one size at a time, and riding the bike normally for a set period of time. That way you can notice the difference under your normal riding conditions.
This is the long way. The quick method is to put the bike on a dyno, make a base run, change the jets, make another dyno run, change the jets again, and keep the process going over and over until the bike makes max power under controlled conditions.
Only problem with this method is you are at the mercy of the dealer. Unless you really know the guys who will be working on your bike, how will you know that the bike is perfectly set up? Do you really think they changed the jets 8 times to find the perfect combination? Did the dyno sheet show runs for each jet size that came in the jet kit? What happened to all those other size jets that came in the kit? There should be left over parts...
But the main reason to rejet a bike after making changes to the intake/exhaust systems is to bring the bike back to a proper air/fuel ratio, to produce the maximum possible power, and to also prevent engine damage. You don't need to buy a jet kit to do so. You can always go to the dealer and buy several different sizes of jets, and things can be just as good as the jet kit.
Also, if you make a mistake with installing jet sizes, its usually not as destructive as if you drill out the wrong hole because the instructions were not perfectly clear (or if you just suck at following directions).
BC.