Do you start anticoagulation in a patient with infective endocarditis who also has atrial fibrillation and stroke?   

In the acute phase, no. You have to get CTA or MRI/MRA with contrast to evaluate for hemorrhagic risk associated with mycotic aneurysms. Even without aneurysms, there is an increased risk of hemorrhage. I normally recommend aspirin in atrial fibrillation patients while the infection is being treated...