Mongo repairDatabase procedure
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.