But since you need to apply different xpaths we can do something
similar...might be some scoping problems here (might have to move it
so the <xsl:variable wraps around) but something like this should work
 (although I'm suspicious of the text(), it would seem to me you need
. or something similar).

<xsl:otherwise>
<xsl:variable name="Values"
select="document(Second.xml)/SubConcepts/SubConcept/Value/@name[.=$clsName]"/>
<xsl:variable name="nodeToProcess" select="$Values[1]">
</xsl:otherwise>
</xsl:when>
<<<

<xsl:variable name="nodeToProcess">
   <xsl:choose>
   ...
  </xsl:choose>
</xsl:variable>