In 2006, Long ran the No. 80 for Hover Motorsports at the Daytona 500, but missed the race. He attempted three races for R&J Racing but also failed to qualify for those events. He returned to the Busch Series, driving the No. 23 for Keith Coleman Racing in six races before being replaced, and also ran a Truck Series race for Jim Rosenblum Racing. He attempted a race at Bristol with Long Brothers Racing, but did not qualify. Long joined a new Nextel Cup team, Cupp Motorsports, in the No. 46 Millstar Tools Dodge. Long attempted three races for Cupp, but failed to qualify for each of them. He returned with help from McGlynn to attempt the Ford 400 at the end of 2006, but did not make the race.