Replacing HTML tags using HTMLEditorKit etc.

Hi
Not sure if this is the best place to ask this. I've searched without finding much.
Basically I am trying to create a HTML template system for output. User's can change the templates to change the program output.
The templates are basic HTML with custom tags inserted, that reside in a templates directory. For example, a simple template might be:
<html><body>
<table width="100%"><tr><td width="25%">Here is the output:</td>
<td> <insertOutputHere> </td>
</tr></table>
</body></html>
^^ Users would be able to edit these template .htm files to affect the output .htm files. For instance, changing where the <insertOutputHere> tag is, or formatting the table it is output to.
I am using the Swing HTMLDocument, HTMLWriter, HTMLEditorKit classes to load and parse the .htm files, iterate the tags and replace any custom tags (defined in code) with the program output. I have been able to locate these custom tags no problem, but I don't know how to replace this tag entirely with my output (Which will be formatted HTML string). I have been trying to use the insertBefore, insertAfter methods with limited success. In particular I have an 'include' custom tag which includes other files by recursion - it works except the <include> tag is not removed, and depending on which insert method I use, it usually goes into an infinite loop of parsing the <include> tag WITHOUT removing it, then picking it up again when its done.
Basically I'm looking for any advice as to how to go about COMPLETELY REPLACING these tags with a well structured HTML string. I can post some code if need be but I barely comprehend what I've done, LOL.
TIA

I've looked over my mess of comments :)
setOuterHTML is what I was previously using and it was quite unpredictable at times, as far as I could tell it is very strict with it's requirements for structured HTML (EG no floating line breaks, everything must be "paragraph-ised" which b0rks up the layout) and I can't rely on anyone using/extending these classes to write well structured HTML.
I remember the problems being quite odd, such as the output for one custom tag being displayed twice for some and not at all for others, and while it isn't critical data, it was still displayed in a way that it could be interpreted as correct - I just knew it wasn't.
So I dropped setOuterHTML to try insertAfterEnd - this leaves the tags in there and, like roughly explained above, it would pick up tags infinitely because they were not being replaced.
Here is a relevant method to give a better idea of what I've done:
 public HTMLDocument parseHTMLfile(String filename, Custom_HTML_Tag tags[]) {
 //create a document
 HTMLDocument doc = (HTMLDocument)kit.createDefaultDocument();
 fileDepth++;
 try {
 //read in the file
 BufferedReader rd = new BufferedReader(new FileReader(filename));
 kit.read(rd, doc, 0);
 if (tags != null) {
 //replace tags with page content
 ElementIterator it = new ElementIterator(doc);
 Element e;
 while ((e = it.next()) != null) {
 //look for includes
 if (e.getName().equals("include")) {
 if (fileDepth >= 5){
 //WARNING:
 System.out.println("fileDepth has reached 5, include may be recursive. aborting.");
 continue;
 String href = (String)e.getAttributes().getAttribute(HTML.Attribute.HREF);
 //grab parent of current file (IE the folder in which it sits)
 File f = new File(filename);
 String include = f.getParent() + sep + href;
 f = new File(include);
 if (f.exists()) {
 HTMLDocument htmld = parseHTMLfile(include, tags);
 StringWriter sw = new StringWriter();
 HTMLWriter w = new HTMLWriter(sw, htmld);
 w.write();
 doc.setOuterHTML(e, sw.toString());
 else {
 //couldnt find include file - warning
 for (int i=0; i < tags.length; i++) {
 if (e.getName().equals(tags.getName())) {
//doc.setOuterHTML(e, tags[i].getText());
doc.insertAfterEnd(e, tags[i].getText());
//System.out.println("found tag: " + tags[i].getName() + ": " + tags[i].getText());
catch (BadLocationException ble) {// cant happen?
System.err.println("ERROR (" + 999 + "): Could not parse document " + filename + "; BadLocationException");
System.err.println(ble);
catch (FileNotFoundException fnf) {
System.err.println("ERROR (" + 999 + "): Could not parse document " + filename + "; File not found");
//System.err.println(fnf);
catch (IOException ioe) {
System.err.println("ERROR (" + 999 + "): Could not parse document " + filename + "; I/O Error:");
System.err.println(ioe);
fileDepth--;
return doc;
setInnerHTML kills it with the 'Can not set inner HTML of a leaf' error
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