It is the latest current release that you're running. Actually, the latest update addressed an exploit that I believe can only be implimented by a user on your server, so its unlikely that you was hacked via a cPanel exploit.
More likely is that you're running a vunerable php script (old version of php nuke or phpbb perhaps?)
Whatever software you have running on your website, just make sure that it's patched with the latest updates available.
Best way to restore the server and restore the public_html files from the backup,
1) Restore the system with fresh OS
2) Secure the server after restore
3) restore all the user data from the old drive
4) Restore all the hacked index files
5) keep updating the server from old software