Hi mr shern,
in 5.2 you can replace the substrate with green functions (e.g. multi-layer substrate) and keep the finite PEC gnd plane. Waveguide port may only work at higher feko versions.(I'm not sure) From your diagram, which looks like a microstrip feed. You can create an additonal PEC plate that connects to the ground and the microstrip line. Place an edge port at the interface between the microstrip-line and new plate that you have just created. I know it is not ideal but it should not have significant deviation from measurements. If you still want to keep your finite substrate, you will have to extent the microstripline slightly longer than the substrate and use the same method stated above to feed the microstrip line. (This is shown in the first first diagram in the above mentioned thread) E.g. like a horizontal V connecting the microstripline and ground.
Hope this helps.
Regards,
E7k