I resolved my Access Denied error when trying to SSH into vCenter by following this article:

VMware Knowledge Base

In my case I had set it to /bin/bash/ instead of /bin/bash

But I still have the certificate issue when attempting to get to https://vcsa.domain.com:5480.  It gives me an invalid certificate error and I cannot login.  But if I go to https://vcsa:5480 I can login and see that my certificate is still from my old CA.  Would like to fix this as it is bugging me.  Any ideas are welcome.