Lomax's 1960/1939 version (#302) implies Willie Johnson as the source of the verses:

2. Well old Reuben had a train
Ran from Boston down to Maine,
You could hear the whistle blow a hundred miles,
O Lordy, &c

3. Now you ought to been in town,
When old Reuben's train went down,
You could hear that whistle blow a hundred miles.

...and there is speculation in the notes of Reuben's lynching. By 1967's Hard Hitting Songs however, we're down to the two actual Johnson verses collected in 1939 and it's no longer a train song. When and where the other pre-1960 verses above were collected is not known.