I am still not Greg, but the answer on pairing is that if you clone the drive and do not pull the CableCARD and then you put the cloned drive in, the pairing is preserved. If you boot the TiVo with the clone drive but with the CableCARD removed, you will lose pairing with Motorola M-Cards. Not sure about Cisco/SA cards.
If you pull the CableCARD and let a new drive boot, then decide to put the original drive in, if you boot the original drive with the CableCARD installed, the original pairing is preserved. Again, I can verify this with Motorola M-Cards as that is what Charter uses in my area.
As far as Windows Copy programs, the one I use is from HDDGuru. It is called HDD Raw Copy Tool.
"Delay is preferable to error" - Thomas Jefferson
"If I have seen further it is by standing on the shoulders of Giants" - Sir Isaac Newton