Your methodology is not so correct.You have to do EM simulation with 3 ports in order to obtain 3-port s-parameters.Each port will have standard 50 Ohm .
After obtaining this 3-port s-parameters, you should do a schematic simulation in a any RF simulator by connecting 50 Ohm Port to Single Ended side,100 Ohm to Differential Side for each
So you will obtain practical operating condition for your Balun.Then you have to check S11,S22,S33 Magnitude in dB, S31,S21 Magnitude and Phase
I hope you understand.