Chapter 52 of Roughing It:

"Six months after my entry into journalism the grand “flush times” of Silverland began, and they continued with unabated splendor for three years. All difficulty about filling up the “local department” ceased, and the only trouble now was how to make the lengthened columns hold the world of incidents and happenings that came to our literary net every day.

From Explanatory Notes:  Clemens returned to New York “in an express train ... a distance of nearly twelve hundred miles by the route I came,”  He stays at the Westminster Hotel.

I went up to Hannibal, Quincy and Keokuk, on the Upper Mississippi. The first and the last named are enjoying a sea son of rest, but not refreshment - the railroads have stricken them dead for a year or two, and I cannot help fearing for Quincy also, now that she is going to build a bridge and let her trade cross the Mississippi, and go through without stopping. St. Louis is doing the same, and somebody has got to suffer for it some day, no doubt.

Letter to the Alta California:

St. Louis,
March 15th, 1867.

HAPPY

On the point of departing San Francisco and a return to New York, Twain in his farewell to the west coast offered an image of what he thought the future would bring. It also provides a window on his view of the industrialization occurring in the world around him.  From his impromptu farewell address to San Francisco:

Flora (sternwheel steamer): The ship was built for the company's trade with Marysville, and thus had an exceptionally shallow draft of 11 inches. She was launched in 1865 then acquired by the California Pacific Railroad Company in 1871.

From Sacramento, "They steamed inland on the Flora to Marysville on the Feather River..."  (pg 356 Scharnhorst V1)

From Marysville,  "They then took a stage to Grass Valley..." 

Scharhorst reports that Twain spent the night in Meadow Lake, a mining camp  where Orion had previously lived.  It is currently a ghost town on the map called Summit City.

The trip from San Francisco to Sacramento was made by river boat, Mark Twain choosing this type  of transportation rather than stagecoach not only for nostalgic reasons, remembering his Mississippi steamboat days, but because it was more comfortable, more scenic, and because the boat had a bar.  

(The Trouble Begins at Eight)

Metropolitan Hall in Sacramento on October 11

Tuesday, Aug 13.—Arrived at Carson Sink where Carson river loses itself. It is a beautiful lake, 25 miles long by 15 wide, and 60 miles from Carson City.

Wednesday, Aug. 14,—Arrived at Carson City 580 miles from Salt Lake, or 1700 miles from St. Joseph    (Orion)