The XML files are missing because you've plugins installed in database, but not in the file system. I have no idea how your migration extension works so I have no idea what all was moved over. It sounds like your SP Upgrade did not go well. I highly advise reverting to a backup and following the instructions I've provided above. Otherwise contact SP Upgrade and find out what they do and do not migrate so you can go from there. As it stands the file structure is missing or messed up and the database tables have been altered.
Kyle (Krileon)
Community Builder Team Member
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krileon
