So my machine is running almost great. Just two little nagging issues and I can't think straight to knock them out properly. I've tried heaps of stuff to fix it and I've lost track, so this thread will serve me for two purposes, to have in writing what I have done (helps to narrow it down), and also to get some more heads in on the issue. I got a good head on my shoulders but it doesn't actually know very much in the grand scheme of things.
1) If I set Backup to run a scheduled backup or run a manual backup, the system will freeze up. I can move the mouse around fine, but that is it. Absolutely nothing responds and it does nothing overnight as well, so I have to physically reset the computer. If I run a system image, it works perfectly fine. If I manually copy all my data folders over to the backup drive, it works fine. I have run a diagnostic on the backup drive and it passed.
2) Every now and then if I right-click the mouse I immediately get the notice box "Windows Explorer is not Responding", where explorer then closes and restarts itself. Usually this happens when I have multiple programs running and I wont lose anything, but it's frustrating when I repeatedly can't get the right-click context menu. It often seems to clear up nicely for a while after rebooting...