Justinian closed the Egyptian temple at Philae during his reign, as well as chased out the Neoplatonist philosophers to Persia, so there were still some pagans left in mid-6th century. However how long this last and when were the last ones converted? I know some vestiges of their beliefs lived on in Christianity, but when were the last rites to Zeus, Jupiter or Amon-Ra performed? I read somewhere that some Maniots were still pagan in the 9th century.
hi! Regarding Egypt, you may find something of interest in these posts