right, in the footage folder after you downloaded a youtube video, do you have -.wav ? if yes, then at least ffmpeg is able to extract a wav from the .flv - it means that it should be able to transcode from flv to avi / mov.
maybe only the encoding part needs to be adapted: youscrap.py - line 133
like i said, start pd in a terminal, it should give you more information about the problem.
pat