ABC Navigator does only a subset of ABC and (much more seriously) its author doesn't respond to bug reports. Use abcm2ps instead.

BarFly (for the Mac) will transpose for you. I believe there is a utility called abc2abc for Linux and DOS/Windows that will do source-to-source manipulations like that.

I've never heard the versions you're talking about. There seem to be at least two different ones in ABC on the web.