You should prepare a test structure that has GSSG pads for each port of the transformer in according with your wafer test probes.Look at the mechanical specifications of your wafer test probe.
GSSG means Ground Signal Signal Ground.
Then you should prepare 2 structure for each measurement.One for S31 while Port-2 is terminated with 50Ohm on the wafer
The second one for S32 while Port-1 is terminated with 50 Ohm on the wafer.
But first of all, your must draw a calibration structure to calibrate your VNA.Calibration layout consists of Open,Short and 50 Ohm terminations. And you should repeat this calibration for each port.
After all these, you will have to de-embed the s-parameters of the test pads and lines from s-parameters of the transformer itself that is very difficult if the frequency is very high.
There are many tricks to measure passive component on the wafer.You may find some application docs. about these measurements..