Do I take the train to Reggio and take the ferry from there? Or stop in Villa San Giovanni for the ferry?
They put the train on the ferry, so you can buy a through-ticket to your Sicilian destination.
Note: I heartily disrecommend the night train. It was a miserable, herky-jerky experience in 2015.
i did part of the reverse journey from messina to napoli recently. the fastest trains that go on the ferry are 'interrcity' type. total travel time was about six hours. your trip will be about 81/2 hours. the unique part is the ferry journey. once the couches are loaded on board, the power is disconnected and passengers are allowed to get off and go to the top decks. the view is great (obviously during the day) crossing the narrow straits, especially as you sail past the statue of madonna della lettera inscribed with the latin 'we bless you and your city'. i recommend the train if you are not in hurry for all the advantages rail travel has over flying.