Примерно так должно работать (не проверено)
Element root = doc.getDocumentElement();
XPath xpath = XPathFactory.newInstance().newXPath();
String expression = "/processing-instruction('xml-stylesheet')";
ProcessingInstruction pi;
pi = (ProcessingInstruction)xpath.evaluate(expression, doc, XPathConstants.NODE);
pi.setData("type='text/xsl' href='foo.xsl'");