I'm currently doing the mission Tending the Flames but I won the Stormcloak side of the war and now when I go to the Blue Palace I can't find her and Falk Firebeard tells me to 'Please don't interrupt the court' and I can't complete the mission. Please help.
The interrupting the court thing is probably the intro The Man Who Cried Wolf to avoid possible trouble that should probably be done before Tending the Flames. Elisif can sometimes and for no apparent reason appear on Whiterun Plains (Youtube video showing it here).
Edit - Elsif is still Jarl even if the Stormcloaks win the civil war.