I think below is the way to customize those pages. I realize that those pages are part of a function called function qa_page_routing() found in qa-include/app/routing.php
So, we create a custom file and override that routing function.
function qa_page_routing()
{
if (qa_to_override(__FUNCTION__)) { $args=func_get_args(); return qa_call_override(__FUNCTION__, $args); }
return array(
'account' => 'pages/account.php',
'activity/' => 'pages/activity.php',
'admin/' => 'pages/admin/admin-default.php',
'admin/recalc' => 'pages/admin/admin-recalc.php',
'answers/' => 'pages/answers.php',
'ask' => 'pages/ask.php',
'categories/' => 'pages/categories.php',
'comments/' => 'pages/comments.php',
'confirm' => 'pages/confirm.php',
'favorites' => 'pages/favorites.php',
'favorites/questions' => 'pages/favorites-list.php',
'favorites/users' => 'pages/favorites-list.php',
'favorites/tags' => 'pages/favorites-list.php',
'feedback' => 'pages/feedback.php',
'forgot' => 'pages/forgot.php',
'hot/' => 'pages/hot.php',
'login' => 'pages/login.php',
'logout' => 'pages/logout.php',
'messages/' => 'pages/messages.php',
'message/' => 'pages/message.php',
'questions/' => 'pages/questions.php',
'register' => 'pages/register.php',
'reset' => 'pages/reset.php',
'search' => 'pages/search.php',
'tag/' => 'pages/tag.php',
'tags' => 'pages/tags.php',
'unanswered/' => 'pages/unanswered.php',
'unsubscribe' => 'pages/unsubscribe.php',
'updates' => 'pages/updates.php',
);
}