Wikipedia has noted some of the discrepancies which make such a timeline impossible:
In a first-season episode Adams says the war has been over for five years (suggesting the first season takes place in 1870, although, in "The Major Adams Story", part 1, it is clear that Adams had taken trains west in previous years, commencing "as soon as the war was over").
In season two, reference is made to the war ending six years earlier (1871) and to the presidential nomination of Ulysses S. Grant (1868), a neighbor of Adams before the war and eventually his commanding officer.
In season three (in "The Vincent Eaglewood Story") Grant and Colfax are identified as the current President and VP, which dates it as Grant's first term (March 1869 to March 1873); but also in season three (in "The Countess Baranof Story") the storyline involves the impending sale of Alaska by Russia, but that transaction actually took place in 1867 under Pres. Andrew Johnson.
"The Bernal Sierra Story" (first season) made extensive reference to the ongoing revolution in Mexico pitting Benito Juarez against Maximillian I of Mexico (aka Emperor Maximilian)--but that uprising ended decisively with Maximillian's capture and execution in 1867.
"The Cathy Eckhardt Story" (fourth season, broadcast November 9, 1960) clearly shows the year is 1870, but in "The Charlene Brenton Story" (late third season, broadcast June 8, 1960) reference is made to Bill Hawks' having read the novel Ben-Hur, which was not published until 1880.
The First Transcontinental Railroad was completed in 1869, following approximately the same route as a wagon train from St. Joseph to Sacramento. This would have made wagon trains obsolete by the time most episodes in the series take place; however, little reference is made to railroads in the West during the series.
As long as this is kept in mind, the placement of 'Wagon Train' on the Toobworld timeline should be done on an episode by episode basis. And that would keep it Zonk-free.