When I upgrade MC from one version to another, I always restore a database backup with:
File > Library > Restore Library
That way I do not have to do an import of any of my media. The db restore has all of my original entries. If you can do this, it's a cleaner way to get your MC media back to where it was before your upgrade.
Otherwise, it sounds like many of your files have already been analyzed and that data has been written to the files. That is probably why they are not in the analyze queue. The analyze audio function is known to hang on "bad files". It's a frequent source of trouble during import. I would try to isolate which file(s) are causing the hang using a binary search technique.
I would highlight half of the files that need to be analyzed and try them. If they finish, I'd highlight half of what is left. Continue this until you find the file or files that are causing the hang. You likely have one or more damaged or bad files.
Best of luck.
Brian.