High temperature

My 13 month old son has a high temperature of 40.6, we have been with him in A&E last night and after a 9 hour wait we have been told he has a throat and ear infection, doctor said to keep giving him Calpol and nurofen, now he's temperature is high again, we've tried to give him medicine but he wad sick all over me, what do I do now? Im at braking point, tired, worried etc.. help please