You just need to copy the "system" folder.
As stated in the README file: install.sh is used by the OTA Update feature. It's useless otherwise.
extensions.cfg is still used by the system. If it wouldn't be used, everyone would probably complain @ the pocketbook developers
Maybe you've tried opening a book from the main screen. In that case the system will use the same app which opened that particular book before.
Try opening a new one from the library.
Edit:
Or maybe the book has a format unknown to CR3. As in extensions.cfg, supported formats are: asp, cgi, chm, epub, fb2, htm, html, jsp, mht, php, pl, rtf, txt.