Hello,
The permission restriction to some parts of the system like Shoutbox, Calendar and some other features is not part of the 1.3 release, sadly.
However, the good news is that coming 1.3.1, we're including admin backend to adjust these permissions as you see fit. Only specific parts of the system are covered with this new permission settings, but they should suffice to alter EPESI to anyone's liking.
As for managing groups - it's all done via CommonData (Menu->Administrator->CommonData). In there you can find Contacts and Companies Groups, among other things. Please be wary about deleting entries from those tables, since it may render some of the parts of the system unusable (there should be no errors, but you may end up having no contacts to select from in some fields).
Hope this helps,
Arek