He began running the Cup races in 1999 with the No. 85 Mansion Motorsports team, but DNQ'd for every attempt throughout that year. He ran Bristol again the following year, in the Truck Series posting a career-best 9th place qualifying effort, as well as at Louisville Speedway, where he wrecked very early in the race. After more struggles in 2000, he finally qualified to make his Cup Series debut in one of its most prestigious races, the Coca-Cola 600. However, Darrell Waltrip, one of the top drivers in series history, who was retiring at the end of the 2000 season, failed to qualify. Long gave up his ride to Waltrip for the race. He made another truck race in 2000 at Texas, where he started 33rd but finished 17th in a truck fielded by Team 23 Racing. Long would eventually make his Cup debut at Dover, qualifying 42nd but finishing 41st after a crash on lap 12. He made one more start that year, at Rockingham Speedway, finishing 32nd. He ran three races in 2001, his best finish being a 29th at the UAW-GM Quality 500. He also made his Busch Series debut in 2001 in the Aaron's 312 at Atlanta. Driving the No. 49 for Jay Robinson Racing, Carl started 41st but came across handling problems during the race, relegating him to 42nd.