Railroads from New York to St. Louis, 1867:
Scharnhorst ( The Life of Mark Twain: The Early Years, 1835-1871, page 383) has Twain entering St. Louis after a transfer of trains in Terre Haute. These seems unlikely as the only line to East St. Louis from the east in 1867 was the Ohio and Mississippi. The Indianapolis and St. Louis was the second line to reach St. Louis and it was not completed until 1870.
New Jersey Central: Sam Clemens probably crossed from New York to New Jersey on the Communipaw Ferry, between Communipaw Terminal in Jersey City and Liberty Street Ferry Terminal in Manhattan, then taken the New Jersey Central to Easton. After this I have found no information on his route. What I suggest here is based on the 1861 and 1870 railroad routes plotted in the collection of University of Nebraska kmz files.
Lebanon Valley: From Easton to Bethlehem, the road was acquired by the Reading Company on 20 March 1858, The Lebanon Valley Railroad was chartered in 1836 to build from Reading west to Harrisburg.
East Pennsylvania: From Bethlehem to Reading. It opened a line between ,Reading and Allentown, Pennsylvania, in 1859. The Philadelphia and Reading Railroad, predecessor of the Reading Company, leased the line in 1869.
Philadelphia and Reading Sam’s route may have followed only a short length of track in the town of Reading. The Philadelphia and Reading Railroad (P&R) was one of the first railroads in the United States. Along with the Little Schuylkill, a horse-drawn railroad in the Schuylkill River Valley, it formed the earliest components of what became the Reading Company. Primarily, the P&R was constructed to haul anthracite coal from the mines in northeastern Pennsylvania's Coal Region to Philadelphia.
Philadelphia and Erie Along Sam Clemens’ hypothesized route, the only Philadelphia and Erie track he may have been on was a bridge crossing the Susquehanna River just north of Harrisburg.
The company began as the Sunbury and Erie Railroad Company, chartered by the Commonwealth of Pennsylvania in 1837, to build a rail line between Sunbury and Erie, Pennsylvania. Construction did not begin until the state passed legislation reducing tax assessments, in 1852. By December 1854, 28.5 miles of track were completed between Milton and Williamsport. The line reached Sunbury in 1855, a total of 40 miles. The company continued to experience financial problems, exacerbated by the Panic of 1857. The tracks reached Lock Haven in 1859. To speed completion of the line, the Sunbury & Erie also started building towards the southeast from Erie. That portion of the line reached Warren, a distance of 66 miles, by 1859; little construction occurred in 1860 amid the politics leading to the Civil War.
In 1861 the Pennsylvania General Assembly passed additional legislation to strengthen the company's financial position, and changed the company name to the Philadelphia and Erie Railroad (P&E). Other, related legislation authorized various railroad companies to lease the lines of other companies, and the PRR entered into a 999-year lease with the Philadelphia & Erie in 1862. That same year the PRR assumed control of the P&E. Labor shortages due to the Civil War further delayed construction.
The main line was completed to Erie in October 1864. The P&E opened a large coal transfer terminal at its Lake Erie terminus in 1866. In 1867 the pier at Erie was expanded to handle ore shipments from the midwest. Despite these improvements, the P&E did not thrive, as it faced strong competition from the New York Central Railroad. Over the next three decades the P&E also experienced serious setbacks due to several major floods, storms, a bridge fire, and various operational accidents.
Pennsylvania : From Reading to Pittsburgh. The Pennsylvania Railroad was an American Class I railroad, established in 1846 and headquartered in Philadelphia. By 1882, the Pennsylvania Railroad had become the largest railroad (by traffic and revenue), the largest transportation enterprise, and the largest corporation in the world. Its budget was second only to the U.S. government. The corporation still holds the record for the longest continuous dividend history: it paid out annual dividends to shareholders for more than 100 consecutive years.
Pittsburgh Fort Wayne and Chicago From Pittsburgh to Monaca. It was a major part of the Pennsylvania Railroad system, extending the PRR west from Pittsburgh, Pennsylvania, via Fort Wayne, Indiana, to Chicago, Illinois.
Cleveland and Pittsburgh: From Monaca to Georgetown. The Cleveland and Pittsburgh Railroad was chartered in 1836. Construction was completed in 1852, with additional branch lines to Akron, Ohio and Wheeling, West Virginia.
Pittsburgh Columbus and Cincinnati : From Columbus to Steubenville. The Pittsburgh, Cincinnati, Chicago and St. Louis Railroad, commonly called the Pan Handle Route, was part of the Pennsylvania Railroad system. Its common name came from its main line, which began at Pittsburgh, Pennsylvania, crossed the Northern Panhandle of West Virginia, and continued west to Bradford, Ohio, where it split into a northern line to Chicago and a southern one through Indianapolis, Indiana, to East St. Louis, Illinois.
Little Miami : From Cincinnati to Dayton. The Little Miami Railroad ran from the eastern side of Cincinnati to Springfield, Ohio. By merging with the Columbus and Xenia Railroad in 1853, it created the first through-rail route from the important manufacturing city of Cincinnati to the state capital, Columbus. The LMRR's importance declined later in the 19th century, after three major railroads from the East built lines across the Allegheny Mountains and established east–west transportation systems through the state.
Ohio and Mississippi From Cincinnati to St Louis. It operated between Cincinnati, Ohio, and East St. Louis, Illinois, from 1857 to 1893. The railroad started in 1854 and paralleled the Cincinnati and Whitewater Canal. Its East St. Louis terminal near th Mississippi River was completed in 1857. It was a founding rail line of the Terminal Railroad Association of St. Louis.
On September 17, 1861, during the American Civil War a train carrying union troops fell through a sabotaged bridge a Huron, Indiana, injuring or killing 100.
On October 6, 1866, the Adams Express Company car was robbed by the Reno Gang, brothers John and Simeon Reno, just east of Seymour, Indiana, making off with $13,000. the first train robbery in U.S. history.
Of course, trains had been robbed before the Reno brothers’ holdup. But these previous crimes had all been burglaries of stationary trains sitting in depots or freight yards. The Reno brothers’ contribution to criminal history was to stop a moving train in a sparsely populated region where they could carry out their crime without risking interference from the law or curious bystanders.
Though created in Indiana, the Reno brother’s new method of robbing trains quickly became very popular in the West. Many bandits, who might otherwise have been robbing banks or stagecoaches, discovered that the newly constructed transcontinental and regional railroads in the West made attractive targets. With the western economy booming, trains often carried large amounts of cash and precious minerals. The wide-open spaces of the West also provided train robbers with plenty of isolated areas ideal for stopping trains, as well as plenty of wild spaces where they could hide from the law. Some criminal gangs, like Butch Cassidy’s Wild Bunch, found that robbing trains was so easy and lucrative that for a time they made it their criminal specialty.
https://www.history.com/this-day-in-history/first-u-s-train-robbery