Additional info, I am using WIX 3.0.4827.0
With the following:

<?if $(var.ProcessorArchitecture)=x64?>
  <?define 64bit=yes?>
  <?define ProgramFiles=ProgramFiles64Folder?>
  <?define ProductGuid={YOURGUID-C701-42ab-B252-2D8C869CA7E3}?>
  <?define UpgradeGuid={YOURGUID-C16C-4aeb-B439-F6A42EB6C022}?>
<?else?>
  <?define 64bit=no?>
  <?define ProgramFiles=ProgramFilesFolder?>
  <?define ProductGuid={YOURGUID-4B18-446e-AD6E-35EB81EB56EE}?>
  <?define UpgradeGuid={YOURGUID-9F5B-4271-90B0-7D0C3A6FC4DE}?>
<?endif?>
  <Product Id="$(var.ProductGuid)" Name="MyProduct.ServerSetup" Language="1033" 
Version="1.0.0.0" Manufacturer="MySoftware" UpgradeCode="$(var.UpgradeGuid)">
    <Package InstallerVersion="200" Compressed="yes" 
InstallPrivileges="elevated" Platform="$(var.ProcessorArchitecture)"/>

I didn't get any replies in my e-mail, but noticed there was an actual reply on 
the archive.

If anybody could help I would be most appreciative

Thanks,

Adam
From: Adam Eversole
Sent: Friday, January 23, 2009 2:24 PM
To: 'wix-users@lists.sourceforge.net'
Subject: Adding system wide module to IIS7 on 64-bit OS

I have a setup that installs a system-wide managed-code module in IIS7. I do 
this as follows:

      <Component Id="modulesConfig" 
Guid="{3D0ACDA1-C029-4084-B3F7-51822745A7ED}" Win64="$(var.64bit)">
       <util:XmlConfig Id="addMyHandler" Sequence="4" 
File="[IISINSTALLDIR]Config\applicationHost.config"
            ElementPath="//system.webServer/modules" Name="add" Node="element"
            Action="create" On="install" />
        <util:XmlConfig Id='add_name' Sequence='5' 
File='[IISINSTALLDIR]Config\applicationHost.config'
            ElementId='addMyHandler' Name='name' Value='myHandler' />
        <util:XmlConfig Id='add_type' Sequence='6' 
File='[IISINSTALLDIR]Config\applicationHost.config'
            ElementId='addMyHandler' Name='type' Value='MyHandler.Module, 
MyHandler, Version=1.0.0.1, Culture=neutral, PublicKeyToken=9a9d230324c99377' />

        <util:XmlConfig Id="modulesConfigRemove" Sequence="4" 
File="[IISINSTALLDIR]Config\applicationHost.config"
            ElementPath="//system.webServer/modules" 
VerifyPath="//system.webServer/modules/add[...@name='myHandler'[\]]"
            Name="add" Node="element"
            Action="delete" On="uninstall" />
      </Component>

With the following preprocessor command setting var.64bit:

<?ifdef $(var.ProcessorArchitecture) = x64?>
  <?define 64bit=yes?>
<?else?>
  <?define 64bit=no?>
<?endif?>

This seems to work just fine in 32-bit, but in 64-bit it fails with the 
following error:

Action 14:21:52: ExecXmlConfig.
Error 25541. Failed to open XML file 
C:\Windows\system32\inetsrv\Config\applicationHost.config, system error: 
-2147024786

I can't figure it out, I made sure I have access to the file in elevated mode 
(the elevated prompt comes up), and it works great in 32-bit.

Any ideas? Is there a better way to do this?

Thanks,

Adam

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