I did the upgrade to 10.9.2 on my 2006 Mac Pro after following this thread on MacRumors:
forums.macrumors.com/showthread.php?t=1598176&page=33
Because the 10.9.2 update overwrites that wonderful Tiamo boot.efi, the Mac Pro will not be able to boot from the 10.9.2 system after the update.
You will need to boot the Mac from another hard drive[or mount the hard drive on another Macintosh) and then replace the Tiamo boot.efi in the following 2 places:
System/Library/CoreServices/
usr/standalone/i386/
You may need to make invisible files visible and probably need to change permissions via the terminal to allow the copying over of the Tiamo boot.efi [Have that file available to you somewhere to copy over]
It sounds harder than it is, but it is definitely helpful to have another Mac or iPad to read the thread before you do this in case there any questions. I just followed their instructions.
Good luck.