> Can someone please tell me how I can give elements of a 
> subtree that are copied to the output with <xsl:copy-of 
> select="."> a new namespace?
> 

You can't: xsl:copy-of always copies elements without change.

You need a variation of the identity template which walks the tree
recursively creating new elements whose name is based on the existing name:

<xsl:template match="*">
  <xsl:element name="{local-name()}" namespace="new-namespace-uri">
    <xsl:copy-of select="@*"/>
    <xsl:apply-emplates/>
  </xsl:element>
</xsl:template>

Michael Kay
http://www.saxonica.com/