Revnron >> Migration Assistant ... copied all the files into one file instead of transferring the full directory to the new one
what file type is the Migration Assistant (MA) output (and what is its size in gigabytes) -- a "file" is a different animal than a "directory" (folder)
in my experience -- MA process creates a new directory (folder) in Users that you rename in the MA process and you log into it like any User account -- if you followed the basic directions to bring over all the information from your old Mac User account to the new Mac (or SSD)
simply try logging out and see if the new Migrated user is available to log in (and check your root directory Users folder for user accounts)-- MA process prompts you to rename the new user account and set new user account password -- you may have some issues with outdated apps not working in the new Mac, but MA is generally solid (in my experience)
if you created and preserved the user (in your new macOS install) that user should still be available -- i just trash it as I work from scratch bringing the entire original working User to the new machine (or SSD)
though i may not understand what you mean...