We present an experimental study of pulse dynamics in a mode-locked Er:fiber laser. By injecting a continuous wave laser with sinusoidal intensity modulation into the fiber laser, we are able to modulate the gain. Measuring the response of the pulse energy, central frequency, central pulse time, and phase to the gain modulation allows determination of the parameters that describe their coupling. Based on the experimentally derived parameters, we evaluate the free running comb linewidth and frequency uncertainty with feedback included, assuming quantum noise is the limiting factor. Optimization of fiber lasers is also discussed.