Well for those of you who posted this question only receieve the "do it
yourself" answer, here is the code changes I made to the private
MouseHandler class. It gets the table from via
((TableHeader)MouseEvent.getSource()).getTable() to get the selcted
row's model index (note not selected rows), performs the sort, then
reselects the rows based on the model Index. Works well for me without
any changes to the Table using the sorter.

If anyone has any suggestions on how to tighten this up, please advise.

    private class MouseHandler extends MouseAdapter {
        public void mouseClicked(MouseEvent e) {
            int viewColumn;
            int column;
            int [] modelIndiciesOfSelectedRows;
            JTable table;
            JTableHeader h;
            TableColumnModel columnModel;

            h = (JTableHeader) e.getSource();
            table = h.getTable();
            // JH get selected rows to reset later before canceling and/or
setting sorting status
            modelIndiciesOfSelectedRows = getModelIndiciesOfSelectedRows(table);

            columnModel = h.getColumnModel();
            viewColumn = columnModel.getColumnIndexAtX(e.getX());
            column = columnModel.getColumn(viewColumn).getModelIndex();
            if (column != -1) {
                int status = getSortingStatus(column);
                if (!e.isControlDown()) {
                    cancelSorting();
                }
                status = (status <= 0) ? ASCENDING : DESCENDING;
                setSortingStatus(column, status);
            }

            reselectPreviouslySelectedRows(table,modelIndiciesOfSelectedRows);
        }

        private int [] getModelIndiciesOfSelectedRows(JTable table){
            int [] indicies = table.getSelectedRows();
            int [] modelIndicies = new int[indicies.length];
            for (int i = 0; i < indicies.length;i++){
                modelIndicies[i] =    modelIndex(indicies[i]);
            }
            return modelIndicies;
        }

        private void reselectPreviouslySelectedRows(JTable table, int []
selectedModelIndicies){
            if (selectedModelIndicies.length != 0){
                int selectedRow;
                for(int i = 0; i < selectedModelIndicies.length;i++){
                    selectedRow = getModelToView()[selectedModelIndicies[i]];
                    table.addRowSelectionInterval(selectedRow,selectedRow);
                }
                Rectangle rect = table.getCellRect(table.getSelectedRow(),0,true);
                table.scrollRectToVisible(rect);
            }
        }
    }