Atualizado com o Projeto Wix Completo, de acordo com o craigster

<?xml version="1.0" encoding="UTF-8"?>
<?define SourceDir = "C:\Users\BillSmith\Documents\Visual Studio 2015\Projects\AIS\AIS\bin\Debug" ?>
<?define icon = "C:\Users\BillSmith\Documents\Visual Studio 2015\Projects\AIS\AIS\bin\Debug\1Password.ico" ?>
<?define DesktopFolder = "H:\Desktop" ?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">  
    <Product Id="*" Name="APS" Language="1033" Version="1.3.0.0" Manufacturer="SS" UpgradeCode="890c447c-5a09-4abb-9b01-fadf5e64aad5">
      <Package Id="*" InstallerVersion="200" Compressed="yes" InstallScope="perMachine"
        Description="APS 1.2"
        Comments="APS will assist you with changing your password with a single click!"
        Manufacturer="SS"
        InstallPrivileges="elevated"
        Platform="x86" />

      <MajorUpgrade DowngradeErrorMessage="A newer version of [ProductName] is already installed." />
      <MediaTemplate EmbedCab="yes" />

      <Feature Id="ProductFeature" Title="AutomatedIDSystemInstaller" Level="1">
        <ComponentGroupRef Id="ProductComponents" />
      </Feature>
    </Product>

    <Fragment>
      <Directory Id="TARGETDIR" Name="SourceDir">
        <Directory Id="ProgramFilesFolder">
          <Directory Id="INSTALLFOLDER" Name="APS" />
        </Directory>
      </Directory>
    </Fragment>
    <Fragment>
      <DirectoryRef Id="TARGETDIR">
        <Directory Id="DesktopFolder" />
      </DirectoryRef>
      <Icon Id="Password.ico" SourceFile="$(var.SourceDir)\1Password.ico" />
      <Property Id="ARPPRODUCTICON" Value="Password.ico" />
    </Fragment>

  <!-- The casing of 'ANOTHERLOCATION' and 'WindowsVolume' is very important here.
     Replace 'MyNewDir' with the correct name of the folder you want on
     WindowsVolume.
-->
    <SetDirectory Id="DesktopFolder" Value="H:\Desktop" />


    <!--<Fragment>
    <Component Id="DesktopShortcut" Directory="APPLICATIONFOLDER" Guid="*">
      <RegistryValue Id="RegShortcutDesktop" Root="HKCU"
              Key="SOFTWARE\APS\settings" Name="DesktopSC" Value="1"
              Type="integer" KeyPath="yes" />
      <Shortcut Id="desktopSC" Target="[APPLICATIONFOLDER]APS.exe"
              Directory="DesktopFolder" Name="APS"
              IconIndex="0"
              WorkingDirectory="APPLICATIONFOLDER" Advertise="no"/>
    </Component>
  </Fragment>-->

    <Fragment>
      <ComponentGroup Id="ProductComponents" Directory="INSTALLFOLDER">
        <!-- TODO: Remove the comments around this Component element and the ComponentRef below in order to add resources to this installer. -->
        <!-- <Component Id="ProductComponent"> -->
        <!-- TODO: Insert files, registry keys, and other resources here. -->
        <!-- </Component> -->
        <!--<Component Id="ProductComponents">
        <File Source="$(var.AutomatedIDSystem.TargetPath)" KeyPath="yes">
          <Shortcut Id="APSShortcut" 
                    Name="APS"
                    Advertise="yes" 
                    Description="1-Click to Change all your passwords!" 
                    WorkingDirectory="INSTALLFOLDER" 
                    ShortName="APS"                      
                    Directory="DesktopFolder"/>
        </File>
      </Component>-->


        <Component Guid="{27E3322C-C85D-4451-A06D-21B524878CA0}">

          <File Source="$(var.AutomatedIDSystem.TargetPath)" KeyPath="yes">

            <Shortcut Id="APSShortcut"
                      Name="APS"
                      Advertise="yes"
                      Description="1-Click to Change all your passwords!"
                      WorkingDirectory="INSTALLFOLDER"
                      ShortName="APS"
                      Directory="DesktopFolder" Icon="Password.ico" IconIndex="0" />
          </File>
        </Component>
        <Component Id="HtmlAgilityPack.dll" Guid="{119C78DC-EFE5-4C84-9583-17F3DE341EFC}">
          <File Id="HtmlAgilityPack.dll" Source="$(var.SourceDir)\HtmlAgilityPack.dll" KeyPath="yes" />
        </Component>
        <Component Id="Microsoft.VisualBasic.PowerPacks.Vs.dll" Guid="{D6DBE101-004B-4383-A5F5-7BF16EB0C0FC}">
          <File Id="Microsoft.VisualBasic.PowerPacks.Vs.dll" Source="$(var.SourceDir)\Microsoft.VisualBasic.PowerPacks.Vs.dll" KeyPath="yes" />
        </Component>
        <Component Id="rtools_setup_x64.exe" Guid="{622D3FCF-E3A0-4A12-99B0-E9D7F879CB16}">
          <File Id="rtools_setup_x64.exe" Source="$(var.SourceDir)\rtools_setup_x64.exe" KeyPath="yes" />
        </Component>
        <Component Id="AutomatedIDSystem.application" Guid="{DB61CF4D-E785-44FD-BB95-D19F7D1619FB}">
          <File Id="AutomatedIDSystem.application" Source="$(var.SourceDir)\APS.application" KeyPath="yes" />
        </Component>
        <Component Id="AutomatedIDSystem.exe.config" Guid="{3E1CD5E7-1AF7-47AF-9FE3-30CEC56EF950}">
          <File Id="AutomatedIDSystem.exe.config" Source="$(var.SourceDir)\APS.exe.config" KeyPath="yes" />
        </Component>
        <Component Id="AutomatedIDSystem.exe.manifest" Guid="{07689029-E9E0-47C0-87D7-5A94FC959EDF}">
          <File Id="AutomatedIDSystem.exe.manifest" Source="$(var.SourceDir)\APS.exe.manifest" KeyPath="yes" />
        </Component>
        <Component Id="AutomatedIDSystem.pdb" Guid="{4D3FBB60-6F55-439E-A88B-ADE7AF7A7459}">
          <File Id="AutomatedIDSystem.pdb" Source="$(var.SourceDir)\APS.pdb" KeyPath="yes" />
        </Component>
        <!--<Component Id="AutomatedIDSystem.vshost.application" Guid="{684D3AC6-FC03-4E87-944B-2D897169CDDE}">
        <File Id="AutomatedIDSystem.vshost.application" Source="$(var.SourceDir)\APS.vshost.application" KeyPath="yes" />
      </Component>-->
        <Component Id="AutomatedIDSystem.vshost.exe" Guid="{478284E1-999D-481D-91B4-4F8F15B998A6}">
          <File Id="AutomatedIDSystem.vshost.exe" Source="$(var.SourceDir)\APS.vshost.exe" KeyPath="yes" />
        </Component>
        <!--<Component Id="AutomatedIDSystem.vshost.exe.config" Guid="{099D79F8-370D-40FE-A6C2-0B76B6397FC7}">
        <File Id="AutomatedIDSystem.vshost.exe.config" Source="$(var.SourceDir)\APS.vshost.exe.config" KeyPath="yes" />
      </Component>-->
        <!--<Component Id="AutomatedIDSystem.vshost.exe.manifest" Guid="{48F07333-9C5B-4894-961D-531C26874531}">
        <File Id="AutomatedIDSystem.vshost.exe.manifest" Source="$(var.SourceDir)\APS.vshost.exe.manifest" KeyPath="yes" />
      </Component>-->
        <Component Id="Password.ico" Guid="{99391003-D8EE-4E6A-98E2-393F2ECE09D8}">
          <File Id="Password.ico" Source="$(var.SourceDir)\1Password.ico" KeyPath="yes" />
        </Component>
        <Component Id="setup.bat" Guid="{0460C522-A02B-4C8B-A0EE-34F1AFF677D1}">
          <File Id="setup.bat" Source="$(var.SourceDir)\setup.bat" KeyPath="yes" />
        </Component>

        <Component Id="netframework" Guid="{6BFA9239-38C7-4040-9487-6A5D20315CA7}">
          <File Id="netframework" Source="$(var.SourceDir)\dotnetfx452_full_x86_x64.exe" KeyPath="yes" />
        </Component>

        <!--    <Component Id="DesktopShortcut" Directory="DesktopFolder"> -->
        <Component Id="ApplicationShortcutDesktop" Guid="902B784B-B1F0-4629-AAC9-D46845734248">
          <Shortcut Id="ApplicationDesktopShortcut" Name="AppName" Description="APS" Target="[INSTALLFOLDER]APS.exe" WorkingDirectory="INSTALLFOLDER" />
          <RemoveFolder Id="DesktopFolder" On="uninstall" />
          <RegistryValue Root="HKCU" Key="Software\APS" Name="installed" Type="integer" Value="1" KeyPath="yes" />
        </Component>
        <!--</Component>-->

      </ComponentGroup>
    </Fragment>
  </Wix>

Depois de seguir a direção que o craigster e está fornecendo avisos para a linha 31

 <SetDirectpry Id="DesktopFolder" Value="H:\Desktop" />

o aviso na linha 41 diz

Show Details    Severity    Code    Description Project File    Line
    Error       The Wix element contains an unexpected child element 'SetDirectory'.    Product.wxs 41
    Warning     The element 'Wix' in namespace 'http://schemas.microsoft.com/wix/2006/wi' has invalid child element 'SetDirectory' in namespace 'http://schemas.microsoft.com/wix/2006/wi'. List of possible elements expected: 'Fragment' in namespace 'http://schemas.microsoft.com/wix/2006/wi'. Product.wxs 41

Diga-me o que preciso fazer no meu WIX para criar um atalho no H: \ Desktop

Além disso, o que preciso remover porque é desnecessário / redundante.