Multiple ElasticSearch instances on Same Host in 2.1

Trying to upgrade to ElasticSearch 2.1 with multiple instances on the same server (vertical scaling) but have run into issues with the inability to specify a CONF_FILE anymore (2.0 release notes says it has been removed). I was able to deploy the multiple instances but am unable to set specific settings per node (i.e. cluster_name, node name, shard_size, replicas, etc) these values get set to the generated values from ElasticSearch. I have tried custom CONF_FILE in different directories but get the same results.

I currently override the /etc/elasticsearch/elasticsearch.yml, /etc/elasticsearch/logging.yml, /etc/init.d/elasticsearch-a, /etc/sysconfig/ file, and /etc/security/limits.d/ file.

Is there a way to have these persist per node configuration (elasticsearch-a.yml, elasticsearch-b.yml, elasticsearch-c.yml, etc.)? I missing files that I need to update with the new 2.1 version.