The important point about the size of the waveport is that it should be large enough to capture the field pattern of the transmission line well. But it should not be too large so that higher order modes start propagating. You can once run and plot the fields on the waveport.
Also, waveport should be away from discontinuty.... Make sure the vias are not closer than lambda/4 to the waveports.. You may need to extend the upper lines and then deembed the waveport to the where you want to read the S parameters.
Feel free to navigate the waveport topic on online HFSS help as well. You may find it useful.
You may use lumped port excitation here as well. You can connect the two grounds through a small PEC sheet and create the port between the trace and this little PEC sheet bridging the two grounds.
Regarding Rad boundary, it might be better to leave some distance from the substrate in x direction, and of course enough distance on z direction.