Firefox and Flock are both based on Mozilla browser technology. A standard Firefox install will find plugins by scanning /usr/lib/mozilla/plugins. In this directory are files and symlinks to the shared libraries of the plugins. To get flash and java enabled in Flock it should be a simple matter to create the same symlinks in ~/flock/plugins. Try this:
cp --no-dereference /usr/lib/mozilla/plugins/libflashplayer.so ~/flock/plugins
cp --no-dereference /usr/lib/mozilla/plugins/libjavaplugin.so ~/flock/plugins
Restart Flock and you should be in business.