Deterministic integration of site-controlled quantum dots with photonic crystal waveguides is demonstrated, which allows positioning the dots for optimal overlap with the waveguide modes. The coupling efficiency (β-factor) of quantum dot emission to propagating waveguide modes ranging from 0 to 88% is measured accounting for statistical variations of quantum dot properties. Using site controlled quantum dots permits us to distinguish between the spectral and spatial origins of fluctuations in β. The role of Fabry-Pérot modes that prevent reaching a deterministic coupling between quantum dots and photonic crystal waveguides is revealed, and ways to overcome this problem are proposed. The results are useful for constructing high-flux single photon emitters based on multiplexed single photon sources.