While it may be possible, the best & most reliable fix would
probably be to install the 10.9.4 or 10.9.5 system again...
Seems to me, there is a reluctance to engage in area of
discussion, having read through several of them in ASC.
You could read through instances of the topic of SBBOD
as noted in a search of spinning beachball of death in
google results as this example notes, and test several
of them to see what content most likely may help; and
see if any relate to your situation. Some may have found
an answer that does not require an installation to work.
But you never know what really was wrong in theirs...
https://www.google.com/?gws_rd=ssl#q=mac+os+x+spinning+beach+ball
Anyway, I'm looking at 1:30AM here and haven't slept.
And have written/deleted more than this result indicates.
While you could attempt another go at this topic in ASC
there is not much headway; if you don't have a reliable
and proven backup (one you can run the Mac from) which
in itself can help resolve several issues, realize only a
Time Machine backup isn't enough to restore a system.
Some may say it is, while I suggest a restoration is to re-
build without necessarily going online; from your archives.
You could see what an Apple Authorized Service Provider
(AASP) or Specialist would advise; however some of them
do not always get the situation correct and their failures
could be not unlike that of a novice, on rare occasion. Not
sure if an Apple Store with Genius bar would be of depth;
but they could help reinstall an all new system. It may not
have your content in the computer, so be sure you back up.
If you don't have it, expect nobody else will.
Anyway, the hour is late and I have an early morning ahead.
Good luck & happy computing! 🙂