<p>A 9.5&#xa0;MeV, 15&#xa0;kW, 2π/3 mode S-band traveling wave (TW) electron linac with constant gradient (CG) type accelerating section, integrated with a constant impedance (CI) type bunching section, has been designed and developed at RRCAT for industrial applications. Since this was a new, non-uniform structure combining CI- and CG-type sections, it was prudent to perform end-to-end, three-dimensional (3D) electromagnetic (EM) simulations of the entire structure to validate the design. In this paper, we present a detailed 3D EM simulation of the full-length TW structure, integrated with input and output RF power couplers, using the 3D EM design software CST-MWS, and demonstrate that the desired field magnitude and phase profile are obtained within the integrated structure in the adopted design. The effect of manufacturing errors on the RF reflection and transmission properties of the structure, and on the amplitude and phase profile of the accelerating field in the linac, has been studied. To reduce the effect of geometrical errors on these RF properties, Steele’s perturbation theory based tuning methodology, commonly discussed in the literature, has been adopted, with a refined formulation for field normalization derived in the paper to account for the non-uniformity in such structures. The tuning methodology has been tested in a simulation environment using CST-MWS, where first the geometrical errors are introduced into the structure, followed by estimating and applying the tuning in individual cells. Such studies will be useful for the future development of TW accelerating structures.</p>