Mongodb ReplicaSet Changing Config Format
After a few days of looking at this and testing different things, I found that there was a missing configuration value 


  systemLog.destination: file


I discovered this by running the following command 


  sudo mongod -f /etc/mongod.conf


instead of doing basic service startup commands 


  (i.e. sudo service mongod start...)


It showed the following error:


  BadValue: Can only use systemLog.path if systemLog.destination is to a
  file


A couple of other things as you troubleshoot. Make sure you maintain the mongo file and folder permissions. I was deleting log and config files as I was troubleshooting and did not realize it was not allowing the engine to start a few times. I ran the following commands to correct the permissions

sudo chown -R mongodb:mongodb /var/log/mongodb
sudo chown -R mongodb:mongodb /var/lib/mongodb


I also went through the process of removing one of the secondaries from the replicaSet 

rs.remove("&lt;server&gt;:27017")


and 

rs.reconfig()


Then logging directly to the old secondary that was a stand alone made sure I can access the database as a standalone.

I then readded the system during the changes of the config

rs.add({host: "&lt;servername&gt;"})


Here is the final config file:

net:
    bindIp: [0.0.0.0,&lt;host_name&gt;,127.0.0.1]
    port: 27017
    http:
        enabled: true
        RESTInterfaceEnabled: true
storage:
    engine: wiredTiger
    dbPath: "/var/lib/mongodb"
    journal:
        enabled: false
processManagement:
    fork: false
security:
    keyFile: "/etc/mongod.key"
    authorization: "enabled"
systemLog:
    logAppend: true
    destination: "file"
    path: "/var/log/mongodb/mongod.log"

replication:
    replSetName: "rs0"


I hope this helps someone