Failing installation - Missing system mailbox accounts

Question

I had installed Exchange 2013 SP1 and it seemed to be working correctly. I installed CU7 and everything fell apart. Massive errors all over the place. I gave up and removed all mailboxes, removed the databases, and uninstalled Exchange 2013.  I then
went into ADUC and manually removed the remaining system mailboxes.
I reloaded a brand new install of Server 2012 R2 (same name as previous exchange 2013 install) and I went to install Exchange 2013 again.  I ran it from the GUI and did not run /PrepareSchema or /PrepareAD in advance.  My understanding was that
running the GUI would do this and since the prepare schema switch in particular is unnecessary since the schema was already updated from the previous install I did not worry about it.
Install fails with:
Error:
The following error was generated when "$error.Clear();
          if ( ($server -eq $null) -and ($RoleIsDatacenter -ne $true) )
            Update-RmsSharedIdentity -ServerName $RoleNetBIOSName
        " was run: "Microsoft.Exchange.Management.Tasks.RmsSharedIdentityUserNotFoundException: RMS Shared Identity user FederatedEmail.4c1f4d8b-8179-4148-93bf-00a95fa1e042 not found.
   at Microsoft.Exchange.Configuration.Tasks.Task.WriteError(Exception exception, ErrorCategory category, Object target, Boolean reThrow, String helpUrl)
   at Microsoft.Exchange.Configuration.Tasks.Task.WriteError(Exception exception, ErrorCategory category, Object target, Boolean reThrow)
   at Microsoft.Exchange.Management.Deployment.UpdateRmsSharedIdentity.Link()
   at Microsoft.Exchange.Management.Deployment.UpdateRmsSharedIdentity.InternalProcessRecord()
   at Microsoft.Exchange.Configuration.Tasks.Task.<ProcessRecord>b__b()
   at Microsoft.Exchange.Configuration.Tasks.Task.InvokeRetryableFunc(String funcName, Action func, Boolean terminatePipelineIfFailed)".
So yes the federated mailbox referenced above does not exist.  As I said I thought the install would have run the /PrepareAD steps and created it.  So I try and run the setup /PrepareAD myself to generate the system mailboxes and that fails:
PS C:\Users\administrator.mydomain.local\Downloads\Exchange2013cu7> .\setup /PrepareAD  /IacceptExchangeServerLicenseTerms
Welcome to Microsoft Exchange Server 2013 Cumulative Update 7 Unattended Setup
Copying Files...
File copy complete. Setup will now collect additional information needed for installation.
Mailbox role: Transport service
Mailbox role: Client Access service
Mailbox role: Unified Messaging service
Mailbox role: Mailbox service
Client Access role: Front End Transport service
Client Access role: Client Access Front End service
Performing Microsoft Exchange Server Prerequisite Check
    Configuring Prerequisites                                                                        
COMPLETED
    Prerequisite Analysis                                                                            
FAILED
     A Setup failure previously occurred while installing the HubTransportRole role. Either run Setup again for just thi
s role, or remove the role using Control Panel.
     For more information, visit:
http://technet.microsoft.com/library(EXCHG.150)/ms.exch.setupreadiness.InstallWatermar
k.aspx
The Exchange Server setup operation didn't complete. More details can be found in ExchangeSetup.log located in the
<SystemDrive>:\ExchangeSetupLogs folder.
So looking in the ExchangeSetup.log I find this:
[12/22/2014 23:32:27.0524] [1] User specified parameters:
[12/22/2014 23:32:27.0524] [1] Beginning processing Get-SendConnector
[12/22/2014 23:32:27.0587] [1] Searching objects of type "SmtpSendConnectorConfig" with filter "$null", scope "SubTree" under the root "Administrative Groups".
[12/22/2014 23:32:27.0587] [1] Request filter in Get Task: (&(objectCategory=msExchRoutingSMTPConnector)(|(&(msExchVersion<=1125899906842624)(!(msExchVersion=1125899906842624)))(!(msExchVersion=*)))).
[12/22/2014 23:32:27.0665] [1] Previous operation run on domain controller 'DC1.mydomain.local'.
[12/22/2014 23:32:27.0665] [1] Preparing to output objects. The maximum size of the result set is "Unlimited".
[12/22/2014 23:32:27.0696] [1] Ending processing Get-SendConnector
[12/22/2014 23:32:27.0696] [1] Evaluated [Rule:SendConnectorException] [HasException:False] [Value:"False"] [ParentValue:"System.DirectoryServices.ResultPropertyCollection"] [Thread:41] [Duration:00:00:09.9289411]
[12/22/2014 23:32:27.0696] [1] Finished [Rule:SendConnectorException] [Duration:00:00:09.9444335]
[12/22/2014 23:32:27.0712] [1] Evaluated [Setting:PowerShellExecutionPolicy] [HasException:False] [Value:"False"] [ParentValue:"<NULL>"] [Thread:45] [Duration:00:00:09.9445571]
[12/22/2014 23:32:27.0712] [1] Finished [Setting:PowerShellExecutionPolicy] [Duration:00:00:09.9445571]
[12/22/2014 23:32:27.0712] [1] Evaluated [Rule:PowerShellExecutionPolicyCheckSet] [HasException:False] [Value:"False"] [ParentValue:"<NULL>"] [Thread:45] [Duration:00:00:09.9445571]
[12/22/2014 23:32:27.0712] [1] Finished [Rule:PowerShellExecutionPolicyCheckSet] [Duration:00:00:09.9445571]
[12/22/2014 23:32:27.0727] [1] Finished [Analysis:Prereq] [Duration:00:00:10.2101752]
[12/22/2014 23:32:27.0743] [1] Failed [Rule:InstallWatermark] [Message:A Setup failure previously occurred while installing the HubTransportRole role. Either run Setup again for just this role, or remove the role using Control Panel.]
Stuck.  Can't finish install, can't uninstall.
I should also mention. I have a working Exchange 2007 server in the environment. 

Answer 1

Holy guacamole!  I was able to finish the setup.
When I ran setup /PrepareAD I also ran /PrepareSchema and /PrepareDomain but I did it in the usual order: PrepareSchema first, PrepareAD second and PrepareDomain third. 
I figured, “can’t hurt, might help.”  The schema theoretically should have already been extended when I installed CU7 onto my SP1 install. But as I posted here:
https://social.technet.microsoft.com/Forums/office/en-US/2de87b3f-52e4-4c1c-8f18-421f948d41c3/seemingly-successful-install-of-exchange-2013-sp1-turns-into-many-errors-in-event-logs-after-upgrade?forum=exchangesvrdeploy#697e5abf-180b-4d78-b841-b5a46cb1ee63
that did not go well.
I noticed lots of event log entries on the DC saying the schema had been modified. 
That may be normal even if running PrepareSchema again but I wonder if it was not an indication that the schema had actually not been extended from SP1 to CU7 after all.
What was common to both of these problematic installs of CU7 was that I had simply run setup and not done the preinstall switches. 
The Exchange installation wizard is supposed to do this but I am now wondering if the wizard for CU7 actually does not. 
If CU7 had made the configuration changes on the exchange server without doing whatever changes were necessary from the preinstall switches, that might help explain why it all went wobbly (in the technical sense) after the CU7 install on my first server.
Sadly though I see many of the same error messages in the event log that I was seeing on my first install.