Regarding these issues
a.) You need to run EigenD from inside the .app package otherwise I think it can't find all it's resources. You should see a menu. Are you running it like this?
./tmp/app/EigenD.app/Contents/MacOS/EigenD --stdout --noauto
b.) Yeah it can only run from the Tools menu of EigenD
c.) See a.)
Starting with --noauto flag makes sure that EigenD starts as a blank slate. Or you can set "blank" as the default setup now in EigenD.
If the above things don't work, you can always run the 1.4.8 release and send it commands instead, the osc agent is now part of 1.4.8 proper.