I've done some of that trip (southern Italy down into Athens, Greece). You will love Bari... it's so beautiful in southern Italy.

If you haven't planned the ferry, you can take the boat to Patras, then take a train to Athens, then ride north and follow the coast all the way back around to Athens (headed out of Athens in the direction of Corinth). It is really a scenic route, slightly hilly, but if you break it up into 3 days and ride about 60 km per day (with breaks), you'll arrive in Patras by about noon at the start of the fourth day, then you get your ticket for the ferry back to Bari, and you can comfortably board the boat a few hours later, secure your bike, and hang out in your spot on the boat.

The ferry ride should be fun. If you're not adventurous, just get the bed. Really.

Koffee