A deep infection and then a subsequent extraction of a tooth can leave the area sore for several months - that's how long it will take for the area to fully heal - even though the gum surface may look like it has healed - underneath takes a longer time period. Your shoulder may hurt b/c your bite may have changed as a result of the tooth being extracted - this can affect the neck and cause pain in the shoulder - or the force of the extraction itself could have caused some misalignment in the jaw or neck area.