One thing to consider in moving from iTunes to JRiver is that the libraries work differently regarding files. If I recall, iTunes forces you to have one folder somewhere that iTunes scans for audio files. JRiver allows you to have files in any folder on any drive. For example, I have many thousands of folders on many, many external hard drives that are all imported into MC.
What I'd do, then, is configure Import (Tools-->Import-->Configure Auto-Import), pick your 100 gb folder + choose any of the options there that you want, and click "Run Auto-Import Now" right underneath "Configure Auto-Import." That should find all the rest of your audio files. Then I'd re-import the playlists and see if they match up to what you had in iTunes (not sure if this will work or not, as all my playlists were created in MC, and I've never tried to import them from another application).
Hope that helps. I remember when I got out of the iTunes world that I had to think differently about how libraries and their files work in different applications. JRiver's A LOT more flexible.