Dan complains that the Black Hills Pioneer doesn't publish baseball scores, and mentions that a new league has started a team in Chicago. He's referring to the Chicago Cubs, one of the founding teams of the National League. They played for the first time in 1876.
Doc and Jane really did tend to the people of Deadwood when smallpox broke out. It was documented that Jane helped save the lives of many people in town, along with a description of her rough-and-tumble appearance in Estelline Bennett's Old Deadwood Days.
David Milch disliked the choreographed fight scene between Seth Bullock (Timothy Olyphant) and the Native American warrior (Juddson Keith Linn) created by the stunt coordinators, finding a fist fight unrealistic in this scenario. It was scrapped at the last minute and Linn recalled the native dance and song from his childhood in Oklahoma. Milch proposed Olyphant holding onto the dancing man's leg, causing him to lose his balance instead.
The Lakota warrior whose grave Bullock disturbs is missing his head. Although it is never stated explicitly, the implication is that this is the man whose severed head is brandished in the streets of Deadwood after Al offers a bounty in the pilot episode.
Smallpox was actually one of the very first viruses to have a vaccine developed for it. The first clear documentation of a smallpox vaccine was in China in 1549, doctors would take the scabs off the infected and grind them into a powder. The powder was then inhaled by healthy people who would develop a mild case of the disease and were then immune from it afterwards. In 1796 physician Edward Jenner was the first to demonstrate the effectiveness of using the similar, but far less deadly, cowpox virus to create a vaccine for smallpox. This became the basis for the modern smallpox vaccine, it was first used in North America in 1800. In the United States the vaccine was widely available to anyone that needed it after the passing of the Vaccine Act of 1813, which required that a steady supply of the vaccine be kept on hand in all major cities and military outposts.