How do I verify the integrity of my OSX installation? (Files, versions, and preferences)
Mount both volumes on a Mac and drag both drives into a file comparison tool like Kaleidoscope. It will show file differences as well as hilight files that exist on one folder as opposed to the other folder.

You could also diff a file listing like ls -laR or whatever other flags you prefer to see what differences (excepting file metadata and ACL / special flags that either take other ls flags or are invisible to a simple file listing.) Some people go so far as to create a listing with md5 or other hashes that checksum the actual contents of files, but that's more appropriate for a security scan / configuration management suite like munki or tripwire.

Lots of blogs cover that sort of professional system management like these entries from 318, Inc.