You want to do what I am doing now LOL, you will absolutely NEED Sony Vegas, it is the shit when doing this kind of audio work, I am sync'ing the LD DD 5.1 tracks to the broadcast DD 2.0 tracks for the '97 SE's, it is very tricky work at first but once you get the hang of it, it is pretty fun.
Adywan gave very good tips on how to do this in 1 of my threads, I will see if I can find it and make a link to it.
OK I found the thread, this is the thread and it starts on page 3 about Vegas.
http://originaltrilogy.com/forum/topic.cfm/97-SW-SE-Trilogy-Take-2/topic/10964/page/3/