intercept video upload and run file through ffmpeg to generate flv and thumbnail

I need to allow users to upload video files (avi, quick time, wmv, etc) and to have the site use ffmpeg to convert the file to an flv and generate a thumbnail then make the new flv file available for users to embed with the FLV Embed plugin.

The only way I can think to pull this off is to intercept the upload handling in wp_handle_upload (in wp-admin/includes/file.php) and make system calls to ffmpeg. Is there a better way? None of the video plugins I’ve found can handle doing the conversion the client demands.

Did I mention the project was already 4 days past due before I got the assingment and that I haven’t slept in two days now? Please, God, someone tell me you know how to make this work. :^)