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If you connect ports 1 and 2 to the VNA, you'll get S11, S12, S22, and S21, but you need all the other ports to be terminated in 50 ohms. Like what biff44 said, connect up the VNA in all the possible configurations until you've measured all the parameters in the S-matrix.
Then, you can take all this info into excel and arrange it to the proper touchstone syntax for an .s5p. However, this file structure will be a bit manual intensive to organize for a .s5p. I don't know of any tools to take everything in and write a .s5p, so you might have to write a little code to do it if you don't want to do it the long way.
Re: any tools can obtain 5 port s parameters from only 2 por
Yep, they are not called "S Parameters" unless there is a 50 ohm impedance at each port (assuming you want 50 ohm charaterization impedance). If you left the unused ports open, it would dramatically change the measured values of the two ports you have connected.
You can do this with a 5 port probing station, where 3 of the probes just have a 50 ohm load attached.