Assuming it's a page with a specific URL fragment, just add a custom page via the 'Pages' panel of the 'Admin' interface with the same URL fragment. That way Q2A's app layer will think the page exists and not included the HTTP 404 header. You can then still override the actual content output for the page in an advanced theme.
Or if you want to override this in general, remove the following line from function qa_home_load_ifcategory(...) in qa-page-home.php:
header('HTTP/1.0 404 Not Found');
As for the other issue, the functions for getting info about the current logged in user changed in version 1.2. See the set of functions whose names start with qa_get_logged_in_... in the qa-app-users.php file.