The fabrication of slow wave structures for THz vacuum electronic devices presents substantial technology challenges and requires tight tolerances as the frequency increases. The fabrication of the 0.346 THz backward wave oscillator for plasma diagnostics is in the final phase. It is based on the Double Corrugated Waveguide, fabricated by high accuracy CNC milling. In this paper, the variation of the height due to the bonding process, with respect to the nominal value and effect of the electron beam misalignment along the propagation direction will be discussed, for predicting the eventual impact on performance.