Hi John,
replacing vCenter certificates after 5.1 release has come was always little bit tricky because lots of new components are there (SSO etc.)
Whole process has many manual steps so that's why there is plenty of space to make a mistake.
So that's why VMware come with SSL Automation Tool which simplifies the process in many ways.
Once you have all certificates, private keys and .pem files prepared it's really quick and straightforward to apply them.
No manual steps is needed to refresh trusts between vCenter components everything is done by SSL Automation Tool.
Check it here:
VMware KB: Deploying and using the SSL Certificate Automation Tool 5.5
Only one think is missing in that KB the way how to create .PEM files, although it is simple ...
If you need help with this just ask...
Regards,
Petr