Iis – What would automatically change the .NET framework version of a site in IIS

It should be possible to script such a process, I would probably start with PSH as it has inbuilt XML support and access to .NET (useful for generating new keys if they are being specified).

But the first thing is to get the list of virtual directories at which to start. This is mostly easily done with appcmd:

# Use array constructor to force an array, event with only one result
# format: VDIR "name" (physicalPath:path)
$vdirs = @(C:\Windows\system32\inetsrv\appcmd.exe list vdir)
$vdirs = $vdirs | Where-Object { -not [string]::IsNullOrEmpty($_) } | Foreach-Object -Process {
  if ($_ -match "physicalPath:([^)]+)\)$") {
   $matches[1]
  }
}

At this point $vdirs is an array of folders mapped to IIS.

Within each of these search for web.config files:

$configFiles = $vdirs | Foreach-Object -Process {
  Get-ChildItem -Path $_ -Recurse -Filter "web.config" | Foreach-Object -Process { $_.FullName }
}

Which is an array of the full path names of the web.config files. At this point you can use PowerShell's XML support to examine or update any part of the file you like

It makes IIS point to different root level config files for .NET. These root level files reside within the framework installation folders in %systemroot%\Microsoft.NET\Framework\<version>\CONFIG

IIS looks for config files for itself in %systemroot%\system32\inetsrv\config\applicationHost.config
and for .NET in
%systemroot%\Microsoft.NET\Framework\<version>\CONFIG\machine.config

Changing the .NET Version switches which machine.config get used. For example, changing it to v2.050727 will have it look at %systemroot%\Microsoft.NET\Framework\v2.0.50727\CONFIG\machine.config. Changing to v4.0.30319 will have it look at %systemroot%\Microsoft.NET\Framework\v4.0.30319\CONFIG\machine.config

Applications inherit things from the root level config settings.

Have a look at this article that outlines the config system and shows the configuration hierarchy.