Well I've been using DVD Decrypter to extract the files from my DVD to my hard drive. I end up with a demuxed .m2v file for the video and an .ac3 file for the audio which I mess around with in MPEG Video Wizard. I also end up with a .SUB file for the English subtitles, but I have no idea what to do with it.

If I'm understanding correctly then there is a way for me to edit the SUB file so that the timing gets fixed (because I have altered the runtime by cutting out gratuitous sex and violence!), and then I would have to put the .SUB file back into the video somehow? And make it so that the video forces it to pop up when it's needed?

I am willing to put some time into this. The subtitled scenes are usually no longer than 2 or 3 minutes and so even if I had to type every line out myself it wouldn't be so bad. I just don't know how to edit the subs or put them back into the video when finished. I also don't know how to tell the video to "force" the subs.