Macintosh HD Library did not migrate. What else is missing?

I recently migrated to a new (identical) MBP Retina with the same OS 10.9.3 and chose to migrate everything. When I compared the two computers, I noticed the new one had about 30 GIG less than the old one. I went through with a fine toothed comb and noticed that the additional content I had downloaded for Logic Pro X which is located in Macintosh HD>Library>Audio had not transferred. Then I noticed that a lot of other data within the Library had not been transferred either. How did this happen and what else might be missing? How can I be sure I have everything I need? I thought ticking all the boxes in the migration meant that everything would be transferred.

Migration Assistant occasionally has oops. Try running it again.
Old post, but in this one Apple Support told the OP to run it several times.
Migration Assistant takes several tries?

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