In early July I plan on ferrying from Bari to Corfu, staying two nights in Corfu, and then moving on to Athens. As far as i see it my best options are to get back on the ferry to Patras and then train to Athens. Should i make reservations ahead of time? Is there a better route?
That is probably the most common route, there may be more ferry options to Patras from Corfu than Bari to Corfu, and Patras to Athens can be done by express bus as well as train. None should require reservations. Another option to consider would be flying, Aegean Air flies Corfu to Athens for under 100 Euro.