Yes, you can use Touchstone models for connectors in the IBIS-AMI channel analyzer. I suggest that you use the Touchstone Viewer to check the quality of the S-parameters, Then run a short simulation (one edge) in the oscilloscope to verify that the circuit behaves as expected. Try it with the SI-SPICE simulator. It is the fastest simulator that uses S-parameters. The stalled analysis is most likely in the channel characterization, not in the eye generation.