I specified "Key=F" in my config file, but pedalbear sent a lowerscore key, why?
Because PedalBear sends keysyms. If you want to send upperscore letters, use the combination of Shift+key. I.e. to send a uppercase F, use :
Why can't I send keys to xterm and friends?
Security feature, see http://people.csail.mit.edu/adonovan/hacks/xsendkey.html for more information.
Is it possible to use the combination of a pedal key and a keyboard key, like shift+left pedal down?
Nope. Different devices, do not worth the hassle.