Problems with missing Launch Agents and Daemons
"Usually I would do a clean install" - this is why clean installs are the best way. The time saved by doing an upgrade-install is often negated by the time spent troubleshooting afterwards.

It may be worth running the latest version of Onyx and clearing out both system and user caches, but I'd probably be more inclined to spend the time letting Time Machine backup my home folder while I download the Yosemite installer and make a USB installer from it.

USB install instuctions for anyone in a similar situation...

Get an 8GB USB stick, label it Untitled - you will need to modify the command below if using a different volume name.

Download the 10.10 installer but don't let it run.

Enter the following command in Terminal

sudo /Applications/"Install OS X Yosemite.app"/Contents/Resources/createinstallmedia --volume /Volumes/Untitled --applicationpath /Applications/"Install OS X Yosemite.app" --nointeraction


Wait for the magic to happen. You can then boot from the USB, erase your HD and perform a clean install which works as it should. You can then forget about your existing issues and move on.

It's not a solution to your issue but it may prove quicker doing this than waiting for a proper answer, particularly if time is an issue...