Did you mean that you are using the Perfect E boundary for top and bottom conductors? You can assign the top and bottom conductors as 2D sheets instead of 3D boxes for optimizing the model.
May I know the length of the transmission line along the X-axis?
If you are using a straight section of the transmission line then you can reduce its length by a significant factor and still be able to do the required analysis using the deembed option of the waveport. Please go through the "differential microstrip" example available under the "open examples" (HFSS>Transmission Lines).
Best regards, Praneeth.
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