Handbrake can convert Mpeg2 or .Tivo files? I thought it was only for dvds.Actually, for all practical purposes TiVo-VideoReDo-AutoProcessor (TVAP) already "does it all". It will automatically run a user-supplied batch file to perform the mpeg2-to-mpeg4 encoding using any encoding program with a command-line interface. HandBrake seems to work quite well and a sample batch file for XVID/AVI creation may be downloaded ***here***. The TVAP thread and the readme file give more details.
TVAP does not schedule TTG transfers however. You must use TiVo Desktop or another program to perform the transfers. I've toyed with the idea of adding the TTG transfer function to TVAP but operation with Desktop is pretty convenient so I haven't been too motivated.
I applaud your effort!