Missing System Apps After Downgrade

Hello All -
I recently downgraded from Yosemite BETA back to Mavericks for multiple reasons. During my invite to test Yosemite I followed all instructions, more specifically the backing up of my computer prior to upgrading. I used Time Machine to back up.
Now that I am downgrading, I restored from Time Machine. I have 99% of my stuff back, but I am missing System Preferences from the OS. It simply appears as question mark as seen in the attached image. I see I am also missing Terminal, and possible others. What is the fix?
More Info: When I click on Apple > System Preferences, nothing happens. There is only one account on my computer and I am the Administrator.

Step one is to DL and reinstall the 10.9.4 COMBO update. If that doesn't fix things, DL the full 10.9.4 installer, save a copy, and reinstall it. If neither work, contact Apple since they recommended that you rely on TM for restoration, rather than a bootable backup/clone of your previously good 10.9.4 installation.
iMac refurb (27-inch Mid 2011), OS X Mavericks (10.9.4), SL & ML, G4 450 MP w/Leopard, 9.2.2

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habschi2 wrote:
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