I think that the scenario of special election is in the event of the incapacitation of a house member, if a senator is incapacitated the gov. appoints his replacement till the end of the term.
Not until the end of the term -- only until the next regular election -- 2008. In Johnson's case, that would also be the end of his term (he beat Thune in 2002.)
When Mrs. Carnahan was appointed to replace her dead husband after the 2000 election, she had to run for the remaining term in 2002, when she was defeated by Talent (who, of course, just lost to McCaskill for the full term starting in 2006).