Want to upgrade to Maverick 10.9 from 10.8.5 Mac Mini Server

I have a 2012 Mac Mini server running 10.8.5 with 2 - 1 TB drives. Sadly I have not really set up my server with anything really important. I was hoping to do a fresh install of 10.9 and then be selectve as to what I re-install including a fresh install of the server app. Then I can take my time getting it set up properly. In the past I remember having an issue with permissions I had set on some external drives from an older MAC. Can't remember all the details but if I remember correctly it kept telling me that I did not have permission to access MY files. A real PIA. What should I do to prevent this from happening unless I am remembering the issue incorrectly? Looks like the update is free but the server app is not, correct?
I just want to start fresh without locking myself out of my external DROBO drives where my pictures, music and videos reside.
Any tips or help would be appreciated.
Thanks
-Zack

Download the Mavericks installer (make a copy now, as installation will delete it), and follow this sequence to make an external bootable installer.  Purchase and download Server.app version 3.  Get the local DNS server configured and working first.  Don't use .local as your top-level domain, and preferably use a real and registered domain that you've registered or have permission to use, or a subdomain of a real and registered domain that you have registered or have permission to use.
As for managing the file ownerships and protections on external devices, that's usually done voa chmod and chown commands (and chmod -R and chown -R) at the command line, or via the Get Info command via the GUI.  Usually setting yourself as the owner of the objects is typically enough.

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