I'd say wipe out anything Mail related in Library. So ~/Library/Mail. ~/Library/Mail Downloads and the com.apple.MailMigratorService.plist in Preferences. Also go nuke ~/Library/Containers/com.apple.mail.

Open up the Time Machine backups and restore ~/Library/Mail along with the com.apple.Mail preference in ~/Library/Preferences. And any other Mail related folders from the backup.

This should trigger another run of the migration assistant. The ~/Library/Containers is a new one to me, looks like this may be the sandboxing, and possibly the migration didn't grab everything to put in there for some reason.