I used this to find the correct site id:
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Dim SiteID As Integer
Dim root As New System.DirectoryServices.DirectoryEntry("IIS://" & ServerName & "/W3SVC")

For Each e As System.DirectoryServices.DirectoryEntry In root.Children
If e.SchemaClassName.ToUpper = "IISWEBSERVER" AndAlso CStr(e.Invoke("Get", "ServerComment")).ToUpper = SiteName.ToUpper Then
SiteID = Convert.ToInt32(e.Name)
Exit For
End If
Next

Dim IISAdmin As New System.DirectoryServices.DirectoryEntry("IIS://" & ServerName & "/W3SVC/" & SiteID & "/Root")