It seems you only changed the property of 3 holes. this might not be enough to create strong resonance. They are at the end of simulation curretly. You may need to shift the source and the time monitor to right, and set the time monitor in the region of strong resonance.
In general we should use 3D FDTD. The only exception is, the 3rd dimension is very long, in theory it will be infinitely long if 2D is used.
In general you will need to use override mesh to make sure the discrete mesh is also periodic.
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