The thickness-dependent multimodal nature of three-dimensional (3D) coupled photonic crystal waveguides is investigated with the aim of realizing a medium for controlled optical gap soliton formation in the slow light regime. In the linear case, spectral properties of the modes (dispersion diagrams), location of the gap regions versus the thickness of the 3D photonic crystal, and the near-field distributions at frequencies in the slow light region are analyzed using a full-wave electromagnetic solver. In the nonlinear regime (Kerr-type nonlinearity), we infer an existence of crystal-thickness-dependent temporal solitons with stable pulse envelope and use the solitonic pulses for driving quantum transitions in localized quantum systems within the photonic crystal waveguide. The results may be useful for applications in optical communications, multiplexing systems, nonlinear physics, and ultrafast spectroscopy.