I think that the issue may very well be with location of your documents. The in place upgrade is looking for them in one spot, and they are in another. Just a thought. I have the same data setup as you.
 
In my case, I just wanted to see how the in place upgrade worked. I almost always do clean installs. As for upgrades over clean installs, not everyone has the know-how to do one.  Being in the business of I.T., it can be easy to forget that many/most people have a very limited knowledge of computers, outside of the few apps they use: IE, Office, games, etc.
 
BTW, even with the small amount of time I spent looking for my "missing" files, I was still far ahead, time-wise, with the upgrade, versus reinstalling all my apps.
 
Gary