I am doing some transformation in PHP5, but only pieces.  The end
result is containing the xml version processing instruction, which
would prefer it did not.  Here is the beginning of the XML:

<?xml version="1.0" encoding="UTF-8"?>

 <xsl:output method="xml" version="1.0" encoding="UTF-8" indent="yes"
standalone="yes"/>

  <xsl:output omit-xml-declaration="yes"/>
is what you are looking for.

All output options are described here
  <http://www.w3.org/TR/xslt#output>