> I need all of the other elements to come over as  
> well and I need to rename those elements. 
yes that's what the 
 <xsl:apply-templates select="*[not(self::title or self::subtitle)]"/>
is doing, applying your templates to all the child elements.
Sounds like you don't want document to go to document though so change
 <xsl:copy>  to <D> 

and when I said

> you just need a standard identity template,
read that as "you just need the templates doing whatever transformation
they are doing"

David

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