So I actually figured it out on our end. When you don't specify a field name, in ES 6 and Kibana 6, a default search parameter default_field: "*" is added by Kibana. Even if Kibana did not add that, ElasticSearch would add default_field: "*.*". (**)
To resolve this, we added a copy_to: "all" mapping to all of our fields, and then reconfigured Kibana to useallas thedefault_field`. This resolves the speed issues entirely.
Unfortunately, we don;'t have the mapping quite right yet.. so we are still having issues. I opened up another post about it here: Proper Template Mapping for ES/Kibana 6.2.3
**: https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-query-string-query.html