Four hours after making port, I'm still waiting at immigration. Everyone has been very polite and professional, but my itinerary over the past few months has raised some questions. My advice for anyone contemplating a similar trip is to go from Turkey to Cyprus by ferry, walk to Larnaca, and then catch a flight to Tel Aviv. That would be cheaper and more direct, and would avoid all the hassles involved with the shipping company and Cypriot regulations, not to mention the visit to Lebanon.
Once I have my passport, I'll find a place to stay in Haifa and spend the rest of the day exploring the immediate area. Hopefully there will still be a few hours of daylight by then!