I upgraded dop to Ubuntu 14.04 Trusty Tahr. This is a LTS release, so I will update my server to this version as well, if all goes well.
I followed this article to straighten some things out after the update.
Opened Software & Updates and re-enabled all third party sources that have the remark: "disabled on upgrade to trusty" (or replaced with new versions). In my case owncloud, profile-sync-daemon and Intel graphics drivers.
sudo apt-get install libappindicator1
Apparently it was already installed, but I still have to reboot to see if that fixes the missing dropbox indicator.
gsettings set com.canonical.Unity.Lenses disabled-scopes "['more_suggestions-amazon.scope', 'more_suggestions-u1ms.scope',
'more_suggestions-populartracks.scope', 'music-musicstore.scope', 'more_suggestions-ebay.scope',
'more_suggestions-ubuntushop.scope', 'more_suggestions-skimlinks.scope']"
While deploying, I noticed that my local apache server is not working. In this post it is explained that the default server path is moved from /var/www to /var/www/html. After moving my files with sudo mv /var/www/[!html]* /var/www/html it seems to be working again.