Looked into this today and have set it up as follows:
//mysite/_config.php
// TinyMCE set buttons
HtmlEditorConfig::get('cms')->setOption('theme_advanced_blockformats','p,h1,h2,h3');
HtmlEditorConfig::get('cms')->setOption('theme_advanced_styles','Button=convert-to-button');
HtmlEditorConfig::get('cms')->setButtonsForLine(1,'bold, italic, bullist, numlist, separator, cut, copy, pastetext, separator, sslink, unlink, separator, advcode, fullscreen, styleselect, formatselect');
HtmlEditorConfig::get('cms')->setButtonsForLine(2);
HtmlEditorConfig::get('cms')->setButtonsForLine(3);
// TinyMCE set valid elements (have removed div and span from this list, may be problem with ssimage alignment)
HtmlEditorConfig::get('cms')->setOptions(array(
'valid_elements' => "@[id|class|style|title],#a[id|rel|rev|dir|tabindex|accesskey|type|name|href|target|title|class],-strong/-b[class],-em/-i[class],-strike[class],-u[class],#p[id|dir|class|align|style],-ol[class],-ul[class],-li[class],br,img[id|dir|longdesc|usemap|class|src|border|alt=|title|width|height|align],-sub[class],-sup[class],-blockquote[dir|class],-table[border=0|cellspacing|cellpadding|width|height|class|align|summary|dir|id|style],-tr[id|dir|class|rowspan|width|height|align|valign|bgcolor|background|bordercolor|style],tbody[id|class|style],thead[id|class|style],tfoot[id|class|style],#td[id|dir|class|colspan|rowspan|width|height|align|valign|scope|style],-th[id|dir|class|colspan|rowspan|width|height|align|valign|scope|style],caption[id|dir|class],-h1[id|dir|class|align|style],-h2[id|dir|class|align|style],-h3[id|dir|class|align|style],-h4[id|dir|class|align|style],-h5[id|dir|class|align|style],-h6[id|dir|class|align|style],hr[class],dd[id|class|title|dir],dl[id|class|title|dir],dt[id|class|title|dir],@[id,style,class]",
'extended_valid_elements' => "img[class|src|alt|title|hspace|vspace|width|height|align|onmouseover|onmouseout|name|usemap],iframe[src|name|width|height|align|frameborder|marginwidth|marginheight|scrolling],object[width|height|data|type],param[name|value],map[class|name|id],area[shape|coords|href|target|alt]"
));
// TinyMCE cleanup on paste
HtmlEditorConfig::get('cms')->setOption('paste_auto_cleanup_on_paste','true');
HtmlEditorConfig::get('cms')->setOption('paste_remove_styles','true');
HtmlEditorConfig::get('cms')->setOption('paste_remove_styles_if_webkit','true');
HtmlEditorConfig::get('cms')->setOption('paste_strip_class_attributes','true');