After going through your all edits and a bit of research from me , you want to execute the following command after the publish from the Visual Studio

> C:\Windows\Microsoft.NET\Framework\v4.0.30319\aspnet_regiis -pe "appSettings" -site Default -app "/" 

If I understood right , You can try wrapping the _ItemGroup_ in a Target with _AfterTargets_ set to **AddIisSettingAndFileContentsToSourceManifest**

```
<Target Name="executeinHosts" AfterTargets="AddIisSettingAndFileContentsToSourceManifest">
    <ItemGroup>
      <MsDeploySourceManifest Include="runCommand">
       //here would be your path that need to run after the publish
      </MsDeploySourceManifest>
    </ItemGroup>
  </Target>
```
So in Your case this is how that part should look:

```
<Target Name="executeinHosts" AfterTargets="AddIisSettingAndFileContentsToSourceManifest">
    <ItemGroup>
      <MsDeploySourceManifest Include="runCommand">
         <path>C:\Windows\Microsoft.NET\Framework\v4.0.30319\aspnet_regiis -pe "appSettings" -site $(DeployIisAppPath) -app "/"</path>
      </MsDeploySourceManifest>
    </ItemGroup>
  </Target>
```
***Additional Info:***
* **AddIisSettingAndFileContentsToSourceManifest** target works just right before Web Deploy copying files from local to server.
* **aspnet_regiis** can be run in <target> node by _<Exec>_.

**Example:**

```
<Exec Command="C:\Windows\Microsoft.NET\Framework\v4.0.30319\aspnet_regiis.exe -pef connectionStrings $(ProjectDir)obj\Debug\Package\PackageTmp" WorkingDirectory="$(publishUrl)" />
```

After going through your all edits and a bit of research from me , you want to execute the following...