To use VLC to convert from MOD to MP4 you can use the following command:
vlc -I dummy -vvv "MyVid.mod"
--sout=#transcode{vcodec=h264,vb=1024,acodec=mp4a,ab=192,channels=2,deinterlace}:standard{access=file,mux=ts,dst=MyVid.mp4}
... where:
-I dummy - Does not show the VLC GUI
-vvv - Gives you verbose output
--sout - Specifies the options to use when encoding to MP4
You can see a full list of VLC command line options by running vlc -H
from the command line. There is also a comprehensive list online at https://wiki.videolan.org/VLC_command-line_help
If you don't have VLC installed locally or you want to outsource bulk video conversions you could always consider using a file conversion API such as https://developers.zamzar.com. This service provides a REST'ful API for file conversion, and mod to mp4 is a supported conversion.
Full disclosure: I'm the lead developer for the Zamzar API.