Here is an except of the log from where it's failing.
15:16:15| Info| CrmAction execution time; SetupOutOfBoxImportMaps; 00:00:15.7343665
15:16:15| Info| Executing Install action: Microsoft.Crm.Tools.Admin.SetIsManaged
15:16:15| Info| CrmAction execution time; SetIsManaged; 00:00:00
15:16:15| Info| Executing Install action: Microsoft.Crm.Tools.Admin.SetFiscalSettingsAction
15:16:16| Info| CrmAction execution time; SetFiscalSettingsAction; 00:00:01.1250072
15:16:16| Info| Executing Install action: Microsoft.Crm.Tools.Admin.PopulateDefaultDataForMultiEntitySearch
15:16:23| Info| CrmAction execution time; PopulateDefaultDataForMultiEntitySearch; 00:00:06.2031647
15:16:23| Info| Executing Install action: Microsoft.Crm.Tools.Admin.BulkDeleteSyncWorkflowProcessSessionsSetupAction
15:16:23| Info| CrmAction execution time; BulkDeleteSyncWorkflowProcessSessionsSetupAction; 00:00:00.0781255
15:16:23| Info| Executing Install action: Microsoft.Crm.Tools.Admin.PublishResourceGroupsAction
15:21:44| Info| CrmAction execution time; PublishResourceGroupsAction; 00:05:21.2511344
15:21:44| Info| Executing Install action: Microsoft.Crm.Tools.Admin.PopulateSolutionComponentAction
15:22:09| Info| CrmAction execution time; PopulateSolutionComponentAction; 00:00:25.3126470
15:22:09| Info| Executing Install action: Microsoft.Crm.Tools.Admin.PopulateDependencyNodesAction
15:24:12| Info| CrmAction execution time; PopulateDependencyNodesAction; 00:02:03.1400417
15:24:12| Info| Executing Install action: Microsoft.Crm.Tools.Admin.PopulateDependenciesAction
15:27:28| Error| System.Exception: Error.ActionFailed Microsoft.Crm.Tools.Admin.PopulateDependenciesAction ---> Microsoft.Crm.BusinessEntities.CrmObjectNotFoundException: sdkmessageprocessingstep With Id = 8e443719-f0c3-de11-9993-005056832bae Does Not Exist
at Microsoft.Crm.BusinessEntities.BusinessProcessObject.Retrieve(BusinessEntityMoniker moniker, EntityExpression entityExpression, ExecutionContext context, Int32 languageCode, DatabaseQueryTarget queryTarget)
at Microsoft.Crm.BusinessEntities.BusinessProcessObject.Retrieve(BusinessEntityMoniker moniker, EntityExpression entityExpression, ExecutionContext context)
at Microsoft.Crm.ObjectModel.SdkMessageProcessingStepImageDependencyCalculator.RetrieveAsSystemUser(BusinessProcessObject service, BusinessEntityMoniker moniker, EntityExpression expression, ExecutionContext context)
at Microsoft.Crm.ObjectModel.SdkMessageProcessingStepImageDependencyCalculator.DetermineSolutionInternalDependencies(ExecutionContext context)
at Microsoft.Crm.ObjectModel.DependencyCalculatorBase.DetermineAllDependencies(ICollection`1 records, ExecutionContext context)
at Microsoft.Crm.ObjectModel.DependencyHelperBase.CreateDependencies(ExecutionContext context)
at Microsoft.Crm.Dependency.ComponentCollector.CreateComponentDependencies(Dictionary`2 recordsByComponentType, ExecutionContext context)
at Microsoft.Crm.Dependency.ComponentCollector.ProcessRecords(ExecutionContext context)
at Microsoft.Crm.Tools.Admin.PopulateDependenciesAction.Do(IDictionary parameters)
at Microsoft.Crm.Setup.Shared.CrmAction.ExecuteAction(CrmAction action, IDictionary parameters, Boolean undo)
--- End of inner exception stack trace ---, Error, RetryCancel, Option1
15:29:05| Info| InputResult: Cancel
15:29:05| Info| CrmAction execution time; PopulateDependenciesAction; 00:04:52.9056632
15:29:05| Error| Installer Complete: OrganizationUpgrader - Error encountered
15:29:05| Error| Exception occured during Microsoft.Crm.Tools.Admin.OrganizationUpgrader: Error.ActionFailed Microsoft.Crm.Tools.Admin.PopulateDependenciesAction
InnerException:
Microsoft.Crm.BusinessEntities.CrmObjectNotFoundException: sdkmessageprocessingstep With Id = 8e443719-f0c3-de11-9993-005056832bae Does Not Exist
at Microsoft.Crm.BusinessEntities.BusinessProcessObject.Retrieve(BusinessEntityMoniker moniker, EntityExpression entityExpression, ExecutionContext context, Int32 languageCode, DatabaseQueryTarget queryTarget)
at Microsoft.Crm.BusinessEntities.BusinessProcessObject.Retrieve(BusinessEntityMoniker moniker, EntityExpression entityExpression, ExecutionContext context)
at Microsoft.Crm.ObjectModel.SdkMessageProcessingStepImageDependencyCalculator.RetrieveAsSystemUser(BusinessProcessObject service, BusinessEntityMoniker moniker, EntityExpression expression, ExecutionContext context)
at Microsoft.Crm.ObjectModel.SdkMessageProcessingStepImageDependencyCalculator.DetermineSolutionInternalDependencies(ExecutionContext context)
at Microsoft.Crm.ObjectModel.DependencyCalculatorBase.DetermineAllDependencies(ICollection`1 records, ExecutionContext context)
at Microsoft.Crm.ObjectModel.DependencyHelperBase.CreateDependencies(ExecutionContext context)
at Microsoft.Crm.Dependency.ComponentCollector.CreateComponentDependencies(Dictionary`2 recordsByComponentType, ExecutionContext context)
at Microsoft.Crm.Dependency.ComponentCollector.ProcessRecords(ExecutionContext context)
at Microsoft.Crm.Tools.Admin.PopulateDependenciesAction.Do(IDictionary parameters)
at Microsoft.Crm.Setup.Shared.CrmAction.ExecuteAction(CrmAction action, IDictionary parameters, Boolean undo)
15:29:05| Info| Setting organization state. New state = Failed