The first info message indicates that your structure is not quite in hydrostatic equilibrium, and this may affect the results slightly. You could consider moving the structure in SpaceClaim so that the mass of displaced water is equal to the structural mass.
The error messages are related to the mesh quality checks that the Aqwa solver applies. In the Hydrodynamic Diffraction Analysis Settings, there is an option to 'Ignore Modelling Rules Violations' - you can use this to change the errors to warnings. However, you should only use this option when there is a small proportion of diffracting elements failing the checks.
The Connection Tolerance in the Mesh settings should not need to be changed from the default value. This is only useful where you have surfaces very close together, or close to the water surface, and you do not want the mesh engine to connect them automatically.