Myself and a friend did a similar journey also in a DA40 we went to Thessaloniki but then continued to Armenia.
As for Italy we stopped in Perugia and Brindisi.
The weather from Perugia was terrible for us so ended up off course almost the whole journey but it was very easy to deal with, from Brindisi we followed the coast south and tracked for Corfu as you can't overfly Albania.
I would consider a stop in Corfu, and maybe make the Zakynthos journey in one go.