Creating a set of yaml to create a basic ELK k8s system

ECK does not have support for Logstash; hence why you can't connect it to Elasticsearch with a single line like you would do with Kibana. You can refer to Access Elastic Stack services | Elastic Cloud on Kubernetes [1.2] | Elastic to figure out how to connect non-ECK applications to Elasticsearch (you seem to have done this already).

Have you considered using Filebeat to ship your logs? ECK supports Beats and could make the integration much easier. See Run Beats on ECK | Elastic Cloud on Kubernetes [2.10] | Elastic.