Now I've got a further problem - the second pass is inserting the
values in the id attributes, but it's dropping any other attributes
that are in the result of pass1.

  <xsl:template match="*[@id]">
    <xsl:copy>

      <xsl:attribute name="id">
        <xsl:number level="any" count="*[@id]"/>
      </xsl:attribute>
      <xsl:apply-templates/>
    </xsl:copy>
  </xsl:template>

This copies all attributes, including @id. The xsl:attribute that
follows then adds another @id with the value you want, which overrides
the first one.