While Salonika is nice, if you're looking for a bit more modern of a Jewish experience I'd recommend Tel Aviv. Think like one of the kibbutzim that's moved on with the times, only it's a city instead.
And if you ever get tired of the fast pace and planned-city pretensions there, you can head over to the Jaffa half of the greater metropolis for a place that's a bit more down to earth. Two great tastes, one city, that's how I've always thought about it!
Plus it's on the Levantine Flyer line, which is the best way to get from Antakya to Alexandria. I recommend paying a bit extra and taking at least a full day apiece in Beirut, Haifa, and Tel Aviv-Yafo. And you may as well throw in another two days to see Damascus; I recommend transferring at Beirut for that.
If you decide to head further into the Balkans, though, might I recommend a visit to Sarajevo? It's a beautiful city, especially because it puts the lie to the ravings of the Serbian and Croatian ultranationalists about their "oppressed brothers" in Bosnia and Herzegovina.