You can use Firebug to look at how your Microflow Timer is currently loaded into a form and copy that DOM element into your index.html. It should a link because in that case you were loading in a LinkContainer and the link text was the text that should become the link. In this case you want something like a MicroflowTimer type.
<div zoomdefault="fill" viewerwidth="1100" viewerheight="300"
usecookie="true" tabindex="0" mxid="8329" minzoomlevel="-5"
maxzoomlevel="10" dojotype="ImageViewer.widget.ImageViewer"
cookieexpire="0" focusindex="0" id="ImageViewer_widget_ImageViewer_0"
widgetid="ImageViewer_widget_ImageViewer_0" class=""></div>
Here I'm loading the ImageViewer.widget.ImageViewer and most of the other settings are the input arguments you usually define in the Modeler. Make sure you strip out the mxid="8329" and the widgetid="ImageViewer.widget.ImageViewer" part.
This should get you pretty far along. Do note that this won't work with a widget that needs to be in a dataview, as it won't have an object when in the index.html.
You could try to edit the widget (or file a feature request). It is possible for the widget to insert a new element somewhere in the DOM outside of the contentpane (in which mendix loads its forms) so that once the widget has been opened (just put it on your start page) it stays there (unless the page is manually refreshed in the browser, in which case it should return to the start page again!:).
Besides that, you might also want to look at an option with XMPP if you want to do chat. Polling and creating objects is not very optimal, especially if you have a lot of people doing it.