FYI - One of the links I posted previously had examples on how to read the mouse scroll wheel with an Arduino.
For something similar to the solution you described with the organ pedal you could look into a photo interrupter. The typical example would be to identify coins passing through a slot. I have used these before to detect passing objects, but I don't know if they would work with a partial obstruction etc... You could however use a few of them at key angles on the shaft.
They do come in several sizes, widths etc... but the easiest one to find on the web is the Sharp GP1A57HRJ00Fhttp://www.sharpsma.com/optoelectronics/photointerrupters/GP1A57HRJ00F
Should only be a few bucks apiece.