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when you use full-wave simulation for any structure (your case is a simple one), the result of your simulation should be like the result of fabricated one. this is achievable when you define all elements(such as transmission line, inductor, capacitance, I/O connectors and etc) correctly in your...
second model seems be correct. you do not need to assign two wave port for two sides of your structure, one port is enough. it is important that the boundary condition of the air box in the port side be selected as "incident field" (not "radiation only").