So I am following the instructions here: https://confluence.atlassian.com/adminjiraserver071/running-jira-applications-over-ssl-or-https-802593051.html
And I am good, using wildcard certificate issued from RapidSSL, up to step 15, after importing the certificate issued by Rapid SSL in step 14 when I try import the CA reply I get the error that the publickey of the CA reply doesn't match the public key of the entry using either of the certs issued by Rapid SSL.
If I go onto the next steps running the config.bat I enter the information for the key and alias and I run the check certificate in the key store it finds the certificate and it looks good.
When I go to the site it gives teh error that the certificate is not trusted because it is self-signed.