I noticed some issues with the newly generated certs in my previous update. I have again generated new certs that this time have the Subject correct. I can delete the bad certs that contain errant Principal from /etc/pki/pki-tomcat/alias and import the new ones. Then update the CA Subsystem Certificate in LDAP using ldapmodify and an updatecert.ldif, as well as update the cert and certreq values in /etc/pki/pki-tomcat/ca/CS.cfg.
What I am unclear on is how to fix the certmonger tracking so it isn't tracking the certs with the errant Principal.