Upgrading SCCM 2012 SP1 to R2 and have one secondary site server hung. Looking at the Secondary Site Installation Status - it is still sitting at "Register secondary site server controls", and has not progressed since March 27

I cannot see anything within the logs to indicate a possible issue

Is there a way to get this moving and not have to delete the site and dB?

Errors in ConfigMgrSetup.log file show

INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Creating indexes on CI_CurrentErrorDetails Configuration Manager Setup 3/27/2015 11:56:44 PM 7220 (0x1C34)

INFO: Executing SQL Server script: Create foreign key ci_currenterrordetails_ciid_fk Configuration Manager Setup 3/27/2015 11:56:52 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Create foreign key ci_currenterrordetails_currentcompliancestatus_fk Configuration Manager Setup 3/27/2015 11:56:52 PM 7220 (0x1C34)
INFO: Executing SQL Server script: Create foreign key ci_currenterrordetails_settingid_fk Configuration Manager Setup 3/27/2015 11:56:52 PM 7220 (0x1C34)

CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.BgbServerChannel.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:08:42 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.DmpConnector.DataUpload.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:09:58 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.DmpConnector.MessageDownload.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:09:58 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\Microsoft.ConfigurationManager.DmpConnector.Usersync.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:09:58 AM 7220 (0x1C34)
CTool::RegisterManagedBinary: Failed to register E:\Microsoft Configuration Manager\bin\x64\AMTEnrollmentServiceWrapper.dll with .Net Fx 2.0 Configuration Manager Setup 3/28/2015 12:10:13 AM 7220 (0x1C34)

INFO: Failed to find Antimalware Agent property matching ScanArchivedFiles on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching DefaultActionSevere on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching DefaultActionHigh on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Antimalware Agent property matching DeleteQuarantinedFilesPeriod on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)
INFO: Failed to find Endpoint Protection property matching EventMonitorPolicyBlue on installation media install map, site control data not updated. Configuration Manager Setup 3/28/2015 12:10:44 AM 7220 (0x1C34)

ERROR: Failed to create sideloading activations alert for this site. Configuration Manager Setup 3/28/2015 12:11:14 AM 7220 (0x1C34)
ERROR: Failed to create default alerts. Configuration Manager Setup 3/28/2015 12:11:14 AM 7220 (0x1C34)