You have two ports: FloquetPort1 and FloquetPort2 and each port has two modes
So FloquetPort1 - mode 1 ; FloquetPort1 - mode 2 ; FloquetPort2 - mode 1 ; FloquetPort1 - mode 2
" For wave returned from port 1 " - In general, you need to plot S(FloquetPort1,FloquetPort1). But since you have modes present, if you want to look at the reflection coefficient when FloquetPort1 is excited with mode 1, then plot S(FloquetPort1:1,FloquetPort1:1)
The meaning for this parameter is S(FloquetPort1:1,FloquetPort1:2) - You excited FloquetPort1 with mode 2 and measuring mode 1 at the same port
For Transmission S21 or S(FloquetPort2,FloquetPort1) - You need to plot S(FloquetPort2 : 1 ,FloquetPort1: 1) or S(FloquetPort2 : 2 ,FloquetPort1: 2) - Mode number should be the same.