DJ,
I don't really know a lot about converting file formats and video stuff, but google sent me to this link: http://forum.videohelp.com/threads/325012-Tool-or-command-line-to-batch-remux-x264-acc-mp4-in-flv Gargalash's first post explains a workflow he uses to go from AVI to x264. That's the best I can do on short notice. I'll be glad to keep looking if you like.
Though, if I were to take a stab at something like this, I'd probably use ffmpeg and force myself to learn the command line arguments. From what I understand, ffmpeg is a video/audio alchemist's dream.