The free electron laser facility FLASH at DESY Hamburg operates a low-emittance photoinjector and several acceleration modules with superconducting cavities to produce a high quality electron beam of up to 700 MeV. Since few months, the accelerator is routinely operated with its design RF pulse length of 800 mus instead of the prior length of 70-200 mus. As a result, the activation of components due to dark current emitted by the gun has reached critical proportions. To improve the understanding of dark current transport through the linac, simulations have been conducted with the Astra tracking code. The generated phase space distributions are compared against a detailed 3-dimensional aperture model of the machine with the newly developed ApertureLib toolkit. The results are in agreement with the observed activities. Measures to reduce the activation of components like the planned redesign of the gun section are evaluated.