Following Ian Strathcarron's advice, I consulted the 1861 historical map
of Jerusalem and plotted out what looks like Twain's most likely route
through the Holy Land, from Beiut to Joppa.  I have noted what seems to
be a discrepancy with what is included in the Quaker City Itinerary.
This has the party traveling from Janin or Jenin to Lubban on September
22, 1867, and then on to Jerusalem.  This appears to contradict Twain's
narrative of traveling to Samaria.  It also contradicts some notes Ian
Strathcarron provided me with concerning his travels in the region.

My map can be seen at
http://bscottholmes.com/content/mark-twains-route-through-holy-land