How do you deal with the problem where the locations you click on the touch screen with your stylus differs from the location on the screen that responded to the click? Thanks in advance.

There is the option in the settings menu. You'll be asked to tap the screen in 4points. In my n900 I had to change a bit the position to get it working well.

I tried that already. It is intermittently flipping between correctly and incorrectly calibrated.