HogWild, when you take your bike in for adjustment, you might get him/her to show you how to make little adjustments to the brakes and shifters on the fly--it can make a world of difference in comfort. I tweak something almost every time I ride, because between normal stretching and the jolts and jars of city street riding, no bike will stay in perfect adjustment for long.

It's great that you're seeking the best handlebar position, etc. and not just accepting things as they were handed to you--every rider is different and needs a little different setup. Some handlebar adjustments will alter the way the brakes and shifters respond, of course.