In September 2002, Stimson took over as manager of Grays after the sacking of Craig Edwards, initially as caretaker manager, but after leading the team to its first victory of the season, he was quickly given the job on an ongoing basis. Despite the signing of a number of former top-level players, such as Carl Leaburn and Jason Dozzell, the team escaped relegation by only one point. The following season, however, boosted by a switch to full-time professional status and helped by the goals of Freddy Eastwood, Grays finished in 6th place, sufficient to gain a place in the newly formed Conference South for the 2004–05 season. Grays won the Conference South at the first attempt by a margin of 23 points, thus achieving promotion to the Conference National, the top level of non-league football, for the first time in their history. In the same season, Stimson also led Grays to the FA Trophy Final, where the team beat Hucknall Town in a penalty shoot-out. Grays reached the FA Trophy Final again in the following season, and claimed a second successive win after a 2–0 victory over Woking at Upton Park. In the Conference, Grays finished in third place and qualified for the play-offs for promotion to the Football League, but lost to Halifax Town in the semi-finals.