Hat Ubuntu backup from USB / to another USB

[Dehcbad25]

ok. I have a server that I put together by using a MS Wind PC. It is a very low power (23 watts with 2 1 TB drives in RAID1), but it has a pretty decent file transfer speed.
I originally put it together to have storage space, but since then it grew more into my intranet,, hosting xymon for network monitoring and the helpdesk/ticket management system.
The little PC works great, except that something sometimes kills it.
I was using this to try to setup a hotclone
http://programs.rcrnet.net/backup/
but for some reason it kills both the current install and the backup. I am guessing it makes changes in the boot, or something else. After running it when I restart it tells me the disc have errors and I have to run fsck, which allows me to boot after, but I can't update the system anymore (files are locked)
At the moment I have a clonezilla backup, but as you might guess, this produces some downtime. I am currently running a restore now.
The PC has the following config
sba1: 1TB RAID1:0
sbb1: 1TB RAID1:1
sbc1: 16 GB / ext4 and swap partitions
I also have a 8 GB, that I setup with with all the same install to test the hot backup. I switch the USB drive, so when connected the 8 GB would be the sbc1 drive.
I am an OK Linux administrator. I use it mainly as my work hobby, but I am in no way an expert, but I am willing to try new things
The 16 GB clone takes about 30 minutes total (including restarts) which is not bad, but it is a downtime, and it cannot be scheduled (since it needs to be initiated from a console), so I would like to find an alternative.
Suggestions and crazy ideas are welcome

[Big Booger]

Did you ever figure this out David?