Robert,
Do you have a workstation with enough hdd space to hold all the data of the SME server ? If so, might I suggest trying Darrell May's backup2ws contrib (contribs.org) ? If a single workstation does not have enough space, how about copying some or most of the files in an ibay to one workstation temporarily, remove the files that have been copied from the server, then do backup2ws to another workstation. Restore the backup to the new server (after which the ibays should have been recreated), then copy back the stuff from the other workstation to the ibay(s) ?
Kelvin