I can scan the drives in Coollector, but I end up with thousands of VOB files not associated with the Title Folder.
I wasn't aware of this problem, thank you very much for reporting it. Tomorrow I'll make you an improved version so you can test it and tell me if it works fine.
Coollector often doesn't make the right association with the movie name: i.e., "Something about Mary" was associated with "Something about Mary Magdalene."
It's important to understand that Coollector focuses on the start of the file name to identify the longest matching string. The movie with Cameron Diaz is called "There's Something About Mary", making "Something about Mary Magdalene" a better match.
Let me guess, I have to go through every movie and check to see each one's properly associated before I accept the index.
Yes, it's better to check the scan results before clicking the add button. This way you can fix the file name typos that cause bad associations. If it's not a typo, adding the year to the end of the name can help. If you find a case where you think the algorithm could be improved, you're welcome to report on this forum.
Shouldn't there be a simple way to edit this after the fact?
It's better to edit before the fact. Once you've added, you'll have to remove the video, then either scan it again or associate it manually (with the "play" icon).