Joe your right, alot of time effort and money goes into the design.
People are right to think they can change the performance though, the designers priority may have been different to yours hence the optimum may not be realised for your application. i.e max power at high rpm, vs max torque at low rpm, various noise regs, fuel consumption, smooth throttle response across the rev range.. all are factors each will be differently prioritised......
First question is are you using the system for an application other than that for which it was designed...if the answer is yes (i.e. with an altered state of tune) then a change may be reuired to achieve optimum performance, the next point is to establish what you want to achieve, more torque, more peak power... etc etc....
Then its time to start measurably modifying using base lines and measureables that directly reflect the preformance you are trying to change.... i.e torque, peak power, fuel consumption... etc etc.
Only down side to all of this is with developed sytems there are usually compromises to be made classically we don't create more power we usually move it around the reve range, or we reduce losses making more mower available..... again decsiion is to decie how you wanna use the bike abd what you are looking for...
Bloody good fun fiddling though, although sometimes expensive for less than expected gains, Captains PCIII application is a great example of this...
Happy modding...
