A) Itachis MS is still active otherwise he wouldn't be able to use Amaterasu after the crow came out.hold on guys is itachi mangekyou really gone since he use that justu to take back controll of is body? he awsome and all but now he not goin to be at full power to help bee and naruto against nagato... but we got to admit he sure is one amazing shinobi... another thing how did hell did pain escape the amaterasu? am so lost lost there i guess amaterasu isnt all that grate as they taught.. i cant wait forthe next capter because now that nagato is still under kabuto's control and itachi is in control of is body thing should get pretty interesting from here on in...... for all a u guys didnt u read the manga for before and from way back them, they is no way madara is shisui ok....
B) Pain just used shinra tensei to repeal amaterasu from his undestroyable body.
C) Quite unlikly that Madara is Shisui, but we still dont know how Shisui died exactly, we will wait if Kishi is going to surprise us anyway...