I'm being driven crazy

I have a cpanel reseller account with no shell access and I have a cpanel server, I am trying to import the accounts from the old server but the diskspace keeps screwing up, sometimes only by a couple of mb but sometimes by a couple of hundred. Its assiging files to the user that should be root and its driving me nuts, i dont have time to manually change them all back !!

If i used ftp to take a complete homedir backup or cpanels homedir backup and then manually created their new accounts and imported it, would that work?

Would that copy over their mail and their passwords too?

What about mysql, is that included in the backup or do i have to run the mysql backup as well?