I have attempted to re create a CSR and I have recieved a new certificate.
I created the new CSR using the key.pem file.
I put the new domainname_org.crt and privateKey.pem into Openfire, and get this.
. Error message: Failed to establish chain from reply
I created the new CSR using the following command:
openssl req -out CSR.csr -key privateKey.pem -new
EDIT
I was now able to get it to accept the certificate by doing the following:
1, Providing the correct key pass phrase, and privateKey.pem
2, Copying the domain_org.crt
3, Copying the SecureServerCA.crt under the domain_org.crt
4. Pressing submit
I was told 'Certificate Authority reply was imported successfully.'. However, it did not show up on anything. After restarting Openfire, I am now told that my keystore is currupt. 
....What happened?