I recently migrated from an Exchange 2013 to another Exchange 2013.  The mail is flowing fine, but outlook 2013 was having a problem connecting to the new server.

I think the problem is with the certificate, but I am out of troubleshooting ideas.

I created a new certificate request using the new server, obtained a godaddy wildcard cert and installed it.  But when I go to the external url owa or ecp site at the new server, I can logon but then it gives me a 500.  When I use the name of the system instead of the url it actually lets me connect. 

not sure where or what to look for.

Also, all my apple devices where having problems connecting to the new server giving a "can not verify account" message, but if I restart the IIS and try to connect within 2-3 mins it connects with no problem.

Any ideas would appreciated

Have you checked Event Logs on that CAS? What about running Test-OWAConnectivity from that machine? The CAS should be pulling in events for these errors, please post these.

I ran the test-OWAconnectivity from the new exchange server:

The Service Endpoint "ExchangeLoginUrl" was not found. This Endpoint gets created during setup, but it has been
deleted.
    + CategoryInfo          : NotSpecified: (:) [Test-OwaConnectivity], ServiceEndpointNotFoundException
    + FullyQualifiedErrorId : [Server=(servername),RequestId=6b13303b-b186-4dd7-89fc-c4a25552004f,TimeStamp=2/6/2015 2:36:49
   PM] [FailureCategory=Cmdlet-ServiceEndpointNotFoundException] 76036DBA,Microsoft.Exchange.Monitoring.TestOwaConnectivity.

I will look at the logs, but just wanted to give the quick update.