Eventually fixed the scrollbar problems by deleting and recreating the controls. Somehow the scrollpanes had become disconnected from the text areas, and there seemed to be no way to re-connect them.

Once that was solved, I was able to get back to working on the XML output. I found that I was able to get the text content of a node using the DOM level 3 getTextContent() method, now available in Java 1.6, which simplified getting the reading and lemma text for display. Popping up dialog boxes for choosing whether a variant was substantive or not proved fairly simple, and it was easy to add/remove/modify the value of the type attribute on the <rdg> tags based on the response.

What proved remarkably difficult was serializing the XML back out as text, to go in the textarea for saving. For the record, here's the code I ended up with:

    private String saveDomDocToString(){
        try{
            javax.xml.transform.TransformerFactory transformerFactory =
                            javax.xml.transform.TransformerFactory.newInstance();
            javax.xml.transform.Transformer transformer = transformerFactory.newTransformer();
            transformer.setOutputProperty(javax.xml.transform.OutputKeys.OMIT_XML_DECLARATION, "yes");
            java.io.StringWriter xmlout = new java.io.StringWriter(); 
            javax.xml.transform.stream.StreamResult result = new
                                javax.xml.transform.stream.StreamResult(xmlout); 
            transformer.transform(new javax.xml.transform.dom.DOMSource(doc),result);
            return xmlout.toString(); 
        }
        catch(Exception e){
            JOptionPane.showMessageDialog(this, e.toString(), "Error serializing the XML",                                            JOptionPane.ERROR_MESSAGE);
            return "";
        }
    }

I've tested this fairly thoroughly, even injecting Japanese characters into the input from Collate and seeing them successfully work through to the output, so I think this is robust from the character encoding point of view. Next I need to look at the notes Cara gave me in edited files last week, and see what other concerns remain to be addressed.