Hey Chris,
I've used the procedure below a few times without any problems. Clean install smeserver onto the new drive and just set it up with all the defaults. Then shut down and connect the old drive to the system (make sure the system doesn't boot from the old drive). Then do the following.
1. cd /
2. mkdir /mnt/tmp
3. mount /dev/hdax /mnt/tmp (hdax will be the / partition of the old drive)
4. /sbin/e-smith/db configuration setprop backup Program CopyFromDisk status enabled
5. /sbin/e-smith/signal-event pre-restore
6. /sbin/e-smith/signal-event restore-tape /mnt/tmp
7. /sbin/e-smith/signal-event post-upgrade
8. /sbin/e-smith/signal-event reboot.
If you are super paranoid about something stuffing up and trashing the old drive you could back it up to another drive using dd.
I'm not too sure that this may solve your problems though, if qmail has been disabled in the db then those db settings will probably be transfered across to the new setup. At the end of the day you may still have to sort out the db settings. Have Fun
Lloyd