When Father Murphy comes to get the kids out with Eli and gives Drew the blackberries, there are at least 6 kids in the cell: Drew, Ephram, Will, Stanley (Jimmy Mair), and two unnamed older and younger blond boys. Father Murphy then tells the warden, "I would be willing to look after them, but you would have to sign release papers." The warden agrees and tells them to get them "outta here." The very next scene shows Father Murphy and Eli arriving with the all the kids from the cell except Stanley, who was deathly sick. He was so sick, he couldn't have jumped out of the wagon before the scene. In the next scene, where they are dancing, the 3 new kids from the cell (including Stanley) are now gone (the ones Father Murphy signed up to take care of). Stanley disappeared for three shows, then suddenly reappeared in "The Graduation."
When Eli is at the bar, he asks the bartender where Gold Hill is. The bartender says its about 4 miles outside of town, take the north road, take the turn to the LEFT (implying there is a "T"). In the next scene, you see Eli and Drusilla are at the "T" stopping, looking left and right. They see Gage and Murphy coming FROM their left (our right). When asked about the school, Murphy says follow us, which meant it was a right turn at the "T."
Alvin is instructed to write the letter "M" 100 times (which would take some time) while the other kids run out to recess. The scene then switches to a baseball game, and you can see Alvin in the game playing shortstop. Epram then comes out of the school building and comes over to Drew, indicating this happened right after they got recess.