Well assuming that you are going to have the root folder mounted on your new Hard Drive, the only thing that I would do would be to mount your delicate folders on seperate partitions. I mount /home on a seperate partition, and I always backup the /etc folder right after install. Maybe you could use your old hard drive and mount it as /storage, this is also what I do and it works great. Then just put things like your /etc backup on there, and maybe some of your media (or whatever, really up to you.) So in short, I would make sure that you mount your /home/ folder on a seperate partition, and any other folders you deam worthy.
-onelung
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