I don't know anything about dealing with copyright claims personally but we do have a couple clippers here who might have had to go through that stuff, so maybe some of them have answers.
But is that "Content Used" thing saying that Froot made the claim, or just that the claim was made because you used Froot's content? It looks to me it's the latter, though I agree it's still clearly fair use. I think what happened here is that someone (maybe Froot but who knows) saw the video, tipped off higher-ups at Vshojo, Vshojo contacted Muso who they probably already had a contract with, and Muso did the strike since apparently they have experience in doing that sort of thing.
I suggest that you continue to make noise about it and let this Streisand Effect. Maybe contact NuxTaku and see if he'd be willing to help spread the story, though I understand if he and other drama-mongers might think the cheating part of the story is not something they want to touch. Is anyone talking about this on /vt/?