well you're leaving me to guess a lot about your uinput structure, but
I'd guess that 

                   <fo:block id="{@href}">

        			<xsl:for-each select="//TocEntry">
        				<xsl:for-each select="document(@Link)//body">
                			  <xsl:apply-templates/>


just puts in a single id (with possibly empty value) at the top of teh
document
you want an id for each file inclusion so perhaps




        			<xsl:for-each select="//TocEntry">
                                      <fo:block id="{@Link}"/>
        				<xsl:for-each select="document(@Link)//body">
                			  <xsl:apply-templates/>
David

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