My guess is that the "custom" part of the whole thing is for rtorrent.
rutorrent can be upgraded just by replacing its files.
after a quick search I saw that the module is installed in /raid/data/module/RTORRENT
and also saw that there is a /raid/data/module/RTORRENT/www/ directory.
My guess is that under /raid/data/module/RTORRENT/www/ are the files for rutorrent. I believe that if you extract 3.4 version there, overwriting the old files and 3.4 version of the plugins in /raid/data/module/RTORRENT/www/plugins you should be OK.. Just make sure that you don't overwrite file conf/config.php since it may have settings specifically for the Thecus. You can compare the default one and the one you have and see if there are differences. I can't help further here.. (tried to download the module to see myself if I could offer more insight but rapidshare reports file not found)
So it is just an educated guess, since I don't own a Thecus, I suggest that you backup the old installation first and/or seek for advice in upgrading (just rutorrent) in the module's thread at thecus forums
Hope I helped
Good luck