If you managed to recover the data from your sync folder, everything should be there. You may need to restart the computer, as I have had to do this before when migrating Alfred2 and it 'seemed' like the settings and workflows didn't take.
Which "Shared" folder are you referring to? By default, Alfred should be saving all his preferences in ~/Library/Application Support/Alfred 2/. That is assuming you were using Alfred 2 before. Check that location for the Alfred.alfredpreferences file. If it exists, copy it, go to that location on the new user account, delete the existing preferences file and replace it with the copy of the old file. Be sure to take ownership of the file to ensure you have permissions to it.
