Shifted contour auxiliary field Monte Carlo is implemented for molecular electronic structure using a plane-waves basis and norm conserving pseudopotentials. The merits of the method are studied by computing atomization energies of H-2, BeH2, and Be-2. By comparing with high correlation methods, DFT-based norm conserving pseudopotentials are evaluated for performance in fully correlated molecular computations. Pseudopotentials based on generalized gradient approximation lead to consistently better atomization energies than those based on the local density approximation, and we find there is room for designing pseudopotentials better suited for full valence correlation.