So did you turn on ssl from config.inc.php?
See: Configure SSL in OJS
When we went to https, we turned on the forced ssl setting and defined the base_url settings to point to https addresses. Is this what you meant?
edit: but if I understood correctly, your site is running fine, only google scholar is the problem? It could just be that you need to give google some time to adjust to the new url’s, because google regards https as a new url.