Some ideas on this:
The portlet's EDIT mode could use a built-in Tohu questionnaire for configuring the portlet. The VIEW mode would render whichever questionnaire had been configured via EDIT mode.
JSR-286 portlets support AJAX by using serveResource method. This is how the execution server can be accessed.
Getting data in could be done via the portlet session (e.g. by configuring the session attribute name containing the data) or by portlet events.
Submission behaviour could be via sending a portlet event to another portlet, or by extracting the data from the knowledge session and sending it to an external submission url.
Custom CSS/Javascipt should probably all just live in the portal theme.
Configuration of the rule-set could be as simple as pasting the entire <change-set> XML into the configuration UI. But we should also consider versioning of forms which would probably be easier if the rules-set was specified as a single URL.
If the war is generic then any Java classes required by the rules would presumably have to be in the shared classpath of the portal.
The end result will be to provide similar functionality to the IBM Forms Portlet (http://www-10.lotus.com/ldd/lfwiki.nsf/dx/Form_View_Portlet) so looking at this may give some ideas.