The present study has been carried out under the Mega-float Project as one for developing an accurate general-purpose three-dimensional computer program for hydroelastic responses of Very Large Floating Structures (VLFSs) due to wave action in water area with complicated geometry close to the real situation. In the first report, a versatile and powerful approach for wave hydrodynamic loading was newly presented, based on a hybrid finite/infinite element formulation of domain decomposition type, and test calculations gave good results coincident with the existing measured and calculated ones. The present paper describes, in detail, such computational improvements and programming techniques adopted in the computer program to enhance its computability to the resulting large-scale models, as 1) the utmost reduction of the localized computational domain, 2) the application of domain decomposition algorithm, composed of the introduction of hybrid prism elements with the domain-wise vertical orthogonal eigenfunction expansions, and planar finite elements, and simple and flexible particular solutions corresponding to arbitrary bottom motions of VLFS, 3) the use of the hierarchical finite element technique based on super-elements with hundreds of nodes, formed numerically from blocks of the hybrid elements through the static condensation technique, 4) the final symmetric and block-banded coefficient matrix derived by the introduction of hybrid infinite elements and the proper renumbering and matching of condensed unknowns on an inner fictitious interface. Then, analytical explanation to each implementation have been presented. Additional test calculations have been conducted for a 1200 m model VLFS, changing the terms of vertical eigenfunction expansions, the mesh size, and the location and configuration of the outer fictitious boundary, which have clarified the contribution of each factor to the numerical results. Pilot calculations for a VLFS with partially variable rigidity and the one with L-shaped water plane have been successfully done, thus illustrating the potential of the present methodology.