Being its a server to server transfer with the domain being the same.... why the complicated process of creating a new installation and then merging?
Unless you have a special circumstances the way you should do the transfer is:
Download ALL of the web files (not just wp-content) and database from the old location.
Upload the site files to the web directory on the new server and upload the database to the mysql server on your new server.
IF your database username, password or mysql hostname have changed then update then in wp-config.php.
I've transferred numerous sites like this without issue. I recommend that you clear out your web directory and database and follow the above steps and re-transfer your site.
I suspect that in the method you used some kind of corruption occurred somewhere.