This is getting way beyond my experience
If it were mine, my course of action now would be to
1) physically copy theThunderbird profile to a new location
2) Uninstall Thunderbird
3) Delete all traces of Thunderbird from the Windows user profiles. This would be in multiple locations, some hidden in each profile - and you'd have to include the default and all users profiles as well
4) delete everything related in program files - including the common files subfolder
5) clean out the registry line by line
Then reinstall the program and IMPORT the mailboxes from within the program from the store location-not copy the files back
As to the misplaced stuff, I'd consider forwarding that to myself first so that there would be copies in the inbox