How to deploy ASP.NET Web App to Azure VM using ARM Template and CustomScriptExtension

I am trying to create an ARM template to deploy resources for VM plus auto-deploy ASP.Net web app to VM using CustomScriptExtension. I have created a CustomScriptExtension child resource under VM with code snippet as follow:

           "resources": [
                {
                    "type": "extensions",
                    "name": "CustomScriptExtension",
                    "apiVersion": "2015-06-15",
                    "location": "[resourceGroup().location]",
                    "dependsOn": [
                        "[concat('Microsoft.Compute/virtualMachines/', parameters('virtualMachineName'))]"
                    ],
                    "properties": {
                        "publisher": "Microsoft.Compute",
                        "type": "CustomScriptExtension",
                        "typeHandlerVersion": "1.8",
                        "autoUpgradeMinorVersion": true,
                        "settings": {
                            "fileUris": [
                                "<my_storage_file_path>/webdeploy.ps1"
                            ],
                            "commandToExecute": "powershell.exe -ExecutionPolicy Unrestricted -File webdeploy.ps1"
                        }
                    }
                }
            ]

Here's the powershell script for webdeploy.ps1:

    # Install IIS (with Management Console)
    Install-WindowsFeature -name Web-Server -IncludeManagementTools

    # Install ASP.NET 4.6
    Install-WindowsFeature Web-Asp-Net45

    # Delete contents of wwwroot
    Remove-Item -Recurse C:\inetpub\wwwroot\*

    # Install Web Management Service (enable and start service)
    Install-WindowsFeature -Name Web-Mgmt-Service
    Set-ItemProperty -Path  HKLM:\SOFTWARE\Microsoft\WebManagement\Server -Name EnableRemoteManagement -Value 1
    Set-Service -name WMSVC -StartupType Automatic
    if ((Get-Service WMSVC).Status -ne "Running") {
        net start wmsvc
    }

    # Install Web Deploy 3.6
    # Download file from Microsoft Downloads and save to local temp file (%LocalAppData%/Temp/2)
    $msiFile = [System.IO.Path]::GetTempFileName() | Rename-Item -NewName { $_ -replace 'tmp$', 
                 'msi' } -PassThru
   Invoke-WebRequest -Uri http://download.microsoft.com/download/0/1/D/01DC28EA-638C-4A22-A57B-4CEF97755C6C/WebDeploy_amd64_en-US.msi -OutFile $msiFile
   # Prepare a log file name
   $logFile = [System.IO.Path]::GetTempFileName()
   # Prepare the arguments to execute the MSI
   $arguments= '/i ' + $msiFile + ' ADDLOCAL=ALL /qn /norestart LicenseAccepted="0" /lv ' + $logFile
   # Sample = msiexec /i C:\Users\{user}\AppData\Local\Temp\2\tmp9267.msi ADDLOCAL=ALL /qn/norestart LicenseAccepted="0" /lv $logFile
   # Execute the MSI and wait for it to complete
   $proc = (Start-Process -file msiexec -arg $arguments -Passthru)
   $proc | Wait-Process
   Get-Content $logFile

   #Deploy Web App package
   $WebClient = New-Object -TypeName System.Net.WebClient
   $Destination= "C:\WindowsAzure\WebApplication.zip" 
   #$WebClient.DownloadFile($using:WebDeployPackagePath,$destination)
   $WebClient.DownloadFile("<my_personal_storage_account_web_application_path>.zip",$destination)
   $Argument = '-source:package="C:\WindowsAzure\WebApplication.zip" -dest:auto,ComputerName="localhost", -verb:sync -allowUntrusted'
   $MSDeployPath = (Get-ChildItem "HKLM:\SOFTWARE\Microsoft\IIS Extensions\MSDeploy" | Select -Last 1).GetValue("InstallPath")
   Start-Process "$MSDeployPath\msdeploy.exe" $Argument -Verb runas 

After running the ARM template, all the resources are deployed correctly, but the web app is not deployed to IIS. I checked that the IIS and Web deploy are installed as according to the script. I also see that my web application zip file is downloaded from my storage account to C:\WindowsAzure\WebApplication.zip. Appreciate if anyone can advise me on the correct coding for the #Deploy Web App package part.

I can manually publish my app to the VM from Visual Studio after running the ARM template. But still I want to know how do that in automated way via CustomScriptExtension/powershell

Many thanks in advance.