Recently, mechanical systems such as a high-speed vehicles and railway trains moving on flexible beam structures have become a very important issue to consider. Using the general approach proposed in the first part of this paper, it is possible to predict motion of the constrained mechanical system and the elastic structure, with various kinds of foundation supporting conditions. Combined differential-algebraic equation of motion derived from both multibody dynamics theory and finite element method can be analyzed numerically using a generalized coordinate partitioning algorithm. To verify the validity of this approach, results from the simply supported elastic beam subjected to a moving load are compared with the exact solution from a reference. Finally, parametric study is conducted for a moving vehicle model on a simply supported 3-span bridge.