Its officially over!
I was personally contacted by an executive at Viacom, who explained how my film got mixed into their system. Juxtaposer was in a film festival that was presented by Nicktoons, which is of course a Viacom company. They offered selections of the festival as downloadable content, and Juxtaposer was one of them. They just forgot that Viacom's rights to those films were all nonexclusive. He personally assured me that Viacom is no longer making a claim to my film and YouTube should be sending me documents affirming that shortly.
Thanks again to everyone on my blogs and on the Consumerist! And also, thank you to Viacom who stepped up, admitted their mistake and apologized, within two days. This is definitely a nightmare averted.