WiX Heat.exe Win64 Components - Win64="yes"

Here would be the XSLT-file. Save it as e.g. HeatTransform.xslt:

<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
    xmlns:wix="http://schemas.microsoft.com/wix/2006/wi"
    xmlns="http://schemas.microsoft.com/wix/2006/wi"
  exclude-result-prefixes="wix">

  <xsl:output method="xml" encoding="UTF-8" indent="yes" />

  <xsl:template match="wix:Wix">
    <xsl:copy>
      <!-- The following enters the directive for adding the config.wxi include file to the dynamically generated file -->
      <!--xsl:processing-instruction name="include">$(sys.CURRENTDIR)wix\config.wxi</xsl:processing-instruction-->
      <xsl:apply-templates select="@*" />
      <xsl:apply-templates />
    </xsl:copy>
  </xsl:template>

  <!-- ### Adding the Win64-attribute to all Components -->
  <xsl:template match="wix:Component">

    <xsl:copy>
      <xsl:apply-templates select="@*" />
        <!-- Adding the Win64-attribute as we have a x64 application -->
        <xsl:attribute name="Win64">yes</xsl:attribute>

        <!-- Now take the rest of the inner tag -->
        <xsl:apply-templates select="node()" />
    </xsl:copy>

  </xsl:template>

  <xsl:template match="@*|node()">
    <xsl:copy>
      <xsl:apply-templates select="@*|node()" />
    </xsl:copy>
  </xsl:template>

</xsl:stylesheet>

Then, in your heat-commandline add the parameter -t <PathToYourFile>\HeatTransform.xslt. This will add the Win64-attribute to every component. Additionally I have Platform='x64'-attribute in my WiX source file(s) and add the -arch x64-parameter to the invocation of candle, as you already described in your question.

I also had this problem. Below is what I've done and it helped.

1)

Open .wixproj file in notepad and manually change Condition-s in PropertyGroup-s to be "x64" instead of "x86":

<Platform Condition=" '$(Platform)' == '' ">x64</Platform>
...
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x64' ">
...
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|x64' ">
...

2)

Go to Configuration Manager for the solution and make sure that x64 is chosen as the platform for the Wix project.

Although Heat still generates Component nodes without Win64="yes", but it builds ok and installs to the C:\Program Files!