Using muenching grouping:
Create a key for each fund_by_id
copy the last fund from each key by selecting only those funds whose ID matches the last ID in a key group.
<xsl:key name="funds_by_id" match="Fund" use="id"/>
<xsl:template match="Organization">
<Organization>
<xsl:copy-of select="Fund[generate-id() =
generate-id(key('funds_by_id',id)[last()])]"/>
</Organization>
</xsl:template>