I too have been down this road. Youtube seems to be scared shitless of the content owners (big media). Their take down system makes it very easy to get a video removed and to keep it that way. If there is a "mistake" (e.g. you were granted permission or fair use obviously applies), you are cordially invited to take the issue to a court to resolve it. Since no one is going to spend money on lawyers for a stupid youtube video, the complainant clearly has the upper hand.
If you protest this injustice, you will be told that Youtube doesn't want to get sued again and that the best thing to do is not to source any content at all. They will suggest that you only use all original content to avoid having your videos removed. Seriously. That was their "solution".
Instead I promptly quit using youtube and started posting my videos to other sites like vimeo, and I've had no further cases of my videos being removed.