Well, I haven't made an AMV yet, but I did edit a song using Windows Movie Maker. I've also reassembled a preview clip for Hellgate London with it, so it should do the trick for you.
Clipping I can't help with cause I don't even know what that means .
As for making the music fit, I'm guessing it's just gonna take some fine tuning, patience & time.
Good luck. I'm actually a little curious about how this turns out myself...