Hello Manoranjan,
You are correct that the S-parameter port works only for 3D simulations. In order to do this for a 2D simulation you would need to do this manually. You would set observation lines across the single mode waveguide on the input side and across the multimode waveguide on the output side. You would also set input planes at these same locations.
You would use the input planes (configured for 2D modal)and the built in mode solver to calculate the modes. You would then use these modes with the fields along the observation lines and mode expansion to extract the components in the field for each of the modes. The equations for this are in the OptiFDTD documentation for the S-Parameters.
Scott