Migrating from 3.0.1.6 old server to 3.0.3.3 new server

[dennysp]

Hi,
I have a server that is being retired with 3.0.1.6 and need to move all domains, user accounts and mail to a new one that will be running ISPConfig 3.0.3.3. I've been using rsync to keep backups of the var/www and the /var/lib/mysql folders. Both servers are running the same OS (CentOS 5-64bit) using "The Perfect Server" config.
I would like to know if I can restore these folders and not screw the new installation up. Is there a better/safer way to do it? My config has a lot of domains and email accounts/forwards.

Thanks in advance, and keep up the good work!