Budapest, Hungary
Mark Twain wrote about Hungary in his essay Stirring Times in Austria, published in Harper's Magazine, March 1898. He spent a week in Budapest in March of 1899 and gave a speech in honor of the jubilee celebration of the liberation of the Hungarian press, published as "German for the Hungarians."
Church of the Holy Sepulchre
The Church of the Holy Sepulchre is a church in the Christian Quarter of the Old City of Jerusalem.
Heilbronn, Germany
Heilbronn is a city in northern Baden-Württemberg, Germany. It is surrounded by Heilbronn District and, with approximately 123,000 residents, it is the sixth-largest city in the state.
Heidelberg, Germany
May 5 or May 6 Monday – The Clemens family arrived in Heidelberg, Germany and stayed at the beautiful Schloss Hotel, which overlooked the old castle with its forest setting, the flowing Neckar River, and the distant valley of the Rhine. https://daybyday.marktwainstudies.com/vol-1-section-0036/ Vol 1 Section 0036 – Mark Twain Day By Day
The family returned to Heidelberg for a week in August and September of 1891, before moving to Switzerland.
See Bædeker The Rhine from Rotterdam to Constance, 1873 page 176
Grecian Archipelago - Aegean Islands
The Quaker City passed through the archipelago twice, first on its way to Constantinople from Greece and again returning from the Black Sea en route to Smyrna. Twain remarks on passing between Lemnos and Mytilene.
Greece
The Quaker City sailed through the Greek Islands August 13-17, 1867. It stopped at the harbor of Athens August 14-15, during which Twain broke quarantine to visit the Acropolis.
Germany
France
Isaac Gewirtz, in Mark Twain A Skeptic's Progress, writes of Twain's view of the French Revolution:
Ephesus - Ayassalook
On looking at the map, this location seems to actually correspond to Ayassalook, where the Quaker City party got off the train and took donkeys to Ephesus.
Ephesus was one of the great cities of the eastern Mediterranean during Roman times. It contained the Temple of Diana which was considered one of the Seven Wonders of the World.