Partially resolved the scan not completing issue
Found some information on the plugin forum that AskApache caused problems.
I had this plugin installed, but not activated. Deleted it, and added htaccess rule for /wp-admin/admin-ajax.php - allow from all (Not an ideal solution)
Scan now completes when run manually. That's good enough for me. Still getting the mentioned PHP Warnings in error logs - but I can live with that - WordFence is doing it's job protecting the site.