U do not copy any system files dude.
If cpanel version is same than this would work :
Backup all accounts using shell with one command :
cd /var/cpanel/users
for i in * ; do /scripts/pkgacct $i ; done
Quick Tip to transfer via ssh.
Here a really quick handy way of migrating all your C-Panel accouts if you have root access on both boxes from the command line. I find the WHM migration helper a bit to unreliable
1) Setup the new box and get the DNS servers ready
2) On the old box run
cd /var/cpanel/users
for i in * ; do /scripts/pkgacct $i ; done
cd /home
scp cpmove-*.tar.gz
root@newserver.com:/home
3) Login to the new server
cd /home
ls cpmove*.tar.gz | cut -d\- -f2- | cut -d\. -f1 | while read line ; do /scripts/restorepkg $line ;done
4) That should get all your accounts over and ready
Cheers