In the MSI logs under C:\windows\temp\storefront we see the following exception:
"The process cannot access the file 'C:\inetpub\wwwroot\Citrix\<store name>\web.config' because it is being used by another process."
Prior to running the upgrade use IIS manager to:
1. Stop the CitrixDeliveryServicesResources application pool.
2. Edit the advanced settings of the CitrixDeliveryServicesResources application pool so that its start mode is OnDemand.
3. Deleting the Proxy cache (if present) C:\inetpub\wwwroot\Citrix\<all folders>\App_Data\CtxsWebProxyIconCache\
4. Rename the StoreFront install folder to the latest version under C:\ProgramData\Citrix\Storefront Install. Or remove the StoreFront install folder.
5. Run the installer as an administrator.
6.When the upgrade is complete return the application pool to always running.