For scrolling around a zoomed-in PDF, what happens if you use the 4-way rocker at the bottom of the device? It's rare that I do this, but from memory that was the navigation method.
For configuring new key mappings - are you talking on the device OS proper, or within certain (reading) applications? Describe in more detail what you're trying to do. Things done in either environment aren't necessarily application, or take effect, in the other, if that makes sense.
Have you looked at briss? It's a very useful utility for stripping the white space around the edges of PDF's (search the forums - there's a thread dedicated to this app). I find that if I run my PDF's through briss, then I rarely need to zoom using the e-reader, and consequently greater happiness ensues.