Here are the steps that I used to recover this Windows Server 2008 Enterprise SP2 x64 server:
- Boot from a Server 2008 DVD or a "Diagnostics and Recovery Toolset" (DaRT) 6.0 CD
- Allow Startup Repair to run even though failure is expected
- Select "View advanced options for system recovery" and open the Command Prompt
- Change directory to C:\WINDOWS\WINSXS
- Rename pending.xml to pending.bad, then eject the media and reboot (a BSOD may occur if the server is SAN attached due to the defect described in KB961891 so power-cycle if necessary)
- Attempt to boot Windows normally but don't be surprised to see the STOP 0x3B again (this step is needed to trigger another Startup Repair)
- Boot from the Server 2008 DVD or the DaRT 6.0 CD again
- Startup Repair should work this time so let it run until it finishes, then eject the media and reboot
- Server should now boot into Windows but any attempt to install a Windows update will fail
- Log on and run regedit
- Export the HKEY_LOCAL_MACHINE\COMPONENTS key and save the file to a temporary folder (in the unlikely event you need to rollback the next step)
- Delete the AdvancedInstallersNeedResolving and PendingXmlIdentifier values from the HKEY_LOCAL_MACHINE\COMPONENTS key (see KB946414)
- Reboot one more time to validate the issue has been resolved and Windows is happy :)

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