I would not suggest contacting the copyright holders. That could be very dangerous.
Yes, the new legislation makes it illegal to create backup copies, so yes, having the entire DVD ripped to your harddrive would, indeed, be illegal under the now in place Japanese copyright law.
Trying to show that AMVs fall under the Japanese version of fair use, while it is certainly my opinion, will be very difficult, especially since AMVs might not actually be used as evidence of copyright infringement. They might be used, instead to identify potential copyright infringers to investigate, and since we advocate the ripping of source purchased... I have ripped versions of Japanee DVDs and BDs I paid for scattered across my harddrives, I am currently breaking the letter of the Japanese law.
Of course, I think the law is ridiculous, unenforceable, and unethical. I'm also on a shared LAN in my apartment complex. I do not believe our ISP will be able to tell what uploads/downloads come from what specific apartment/machine without pretty much impounding all of the computers across the entire complex.
This is a giant legal clusterfuck, and I don't think there is going to be any change in behavior, and there is no way for Japan to start putting in prison everyone who uses Share or Bittorrent. The consequences would be to deplete an already badly depleted work force...