MongoDB vs. MongoDB Upstart Jobs on Ubuntu

The solution to this issue was as follows: Starting with the secondary:

Inside of Mongo I ran the following:

db.shutdownServer()
exit

On the command line:

rm -rf /var/lib/mongodb/*
sudo service mongodb start

It then takes a couple of hours to resync. Once resynced I did the following on the primary:

rs.status() //To make sure that the everything was synced
rs.stepDown(9200)
db.shutdownServer()
exit

On the command line I ran:

rm -rf /var/lib/mongodb/*
sudo service mongodb start

Then in Mongo I ran:

rs.status() //To make sure that everything was synced
rs.freeze(0) //To remove the re.stepDown(9200) lock

On the secondary I ran:

rs.stepDown()

Note: If possible, back up all of your data first.

When you create the self signed certificate, you need to use a valid host name in the "Common Name" field, e.g.:

Common Name (eg, your name or your server's hostname) []: host.domain.com

If you want use a domain certificate, you need to change "host" with "*", e.g.:

Common Name (eg, your name or your server's hostname) []: *.domain.com