Respectfully, I think measuring a CM choke is being overly complicated in this discussion. The common mode Z is measured just as if the CM choke was an inductor or capacitor. Either measure it with an S11 measurement (shield to shield leaving the center conductor alone or short the input terminals and output terminals together) across Port 0 or do an S21 Thru method getting the insertion loss and the phase angle (input shield to port 0 center conductor and output shield to port 1 center conductor leaving the center conductor of the coax alone. If bifilar-wound, short the input terminals together at port 0 and the output terminals together at port 1 OR determine which conductor is common to in and out and use that conductor only).
If it is necessary to use port 0 and 1 to measure insertion loss just do an S21 with the CM choke connected as if the core wasn't there as the core is immaterial for a CM choke's loss (not so for a bifilar-wound CM choke because Zo is not well controlled so there will be loss due to mismatch).
73
