try using the e-smith server and gateway backup/restore facility (located in the manager)
the backup will grab all user data and ibay data and store it in a single tar file (store it on one of your client machines).
basically it grabs stuff in directories /home/e-smith/files directory (which includes /users, /ibays, and /primary)
as for the mysql servers, the only recommendation there is to perform a mysqldump, store those files somewhere (client machine).
when you reinstall on the new disk, do a restore from the file on your client machine (replaces user data, ibays, etc.), reinstall your mysql servers, and reload that mysql data.
its possible mysql has better backup routines, i've never done a full-scale one before myself.
and if you decide not to 'go with the latter' I think there are a number of postings in these forums for how to add a second hard disk.
good luck,