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"I've been wrestling with just cloning over my current OSX installation to the newly made Fusion drive"

If your existing installation of the OS has been working without problems, it's probably easiest to just "clone it over", using either CarbonCopyCloner or SuperDuper (CCC is free for 30 days, SD lets you do a "complete" clone for free -- or at least it used to).

With the upcoming 10.8.4 update, a lot of OS files are going to get replaced, anyway...
 
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