Time Machine restore or Migration Assistant


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My primary hard drive in my Mac Pro died the other day. I had noticed some warning flags, so in addition to my time machine backups, I'd used Carbon Copy Cloner to make a copy of my system to a secondary drive on my computer. It worked fine in the interim. However, I don't want to use the secondary disk as my primary startup disk, so I purchased and installed a new drive. In the meantime, I tried some changes to my system while it's been on my secondary drive.

Which way is the best way to get up and running on the new drive? Should/can I use CCC to move the system to the new drive, and then use Time Machine to restore it to it's previous settings (the ones from the initial drive, before I made some changes on the system running on the secondary drive)? Or should I use Migration Assistant to move the system to the new drive?
 
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Personally I prefer a clean install of OSX and then migrate back in, YMMV
 

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