first mustang 3 days ago and problems already

[aparker813]

i bought a 99 gt w/62k on it and it runs real great and i love it except for one really puzzling problem. if i'm going from about 20-45 or 50 (seems to be about the range) it feels like the car is jerking a little or surging might be a better word. whats real strange is that if i turn on cruise control then its as smooth as can be. anybody got any ideas as to what it could be? car is mostly stock except for k&n drop in filter and flowmaster mufflers