If he were unable to serve as Senator, the new majority leader could actually be Sen. Mitch McConnell (R-KY) instead of Sen. Harry Reid (D-NV). South Dakota Governor, Mike Rounds, a Republican, would likely appoint a Republican replacement for Johnson, thus bringing the Senate to a 50-50 tie and giving Vice President Dick Cheney the tie-breaker.
South Dakota law is rather odd.
First, it states that if there is a primary or general election within 6 months of a vacancy for a representative or senator, that the election be held concurrently with those elections. If there is no near term regular election scheduled, then the special election is held with 80 to 90 days of the vacancy.
But then it later states that a election to fill a senate vacancy will be held at the next general election, and that no election be held to replace an appointed Senator whose term ends just after a general election. So in the case of Johnson, there would be no election since his term ends in 2009.
Yeah, I'm not sure if anyone has figured out what would actually happen. In most states, the governor gets to appoint a replacement, and then since the next federal election is when the seat is up, anyways, there might not be a special election (at least Coleman didn't take office early).