0k. I got what you exactly doing.
Let me know your proficiency with MATLAB.
I can help you through the process, but may not be able to write a code, especially.
First of all, you must have Four matrix results including Mag (S11), Phase (S11), Mag (S21), Phase (S21) for all the structures you experimented with.
then calculate
S11=mag (S11) * exp (j*3.14*phase (S11)/180)
S21=mag (S21) * exp (j*3.14*phase (S21)/180)
then follow the rest of the calculations as per the formulae given in the concerned paper, infact I can see that there is an example solved in there, you just need to follow those very steps while creating variables.
Keep in mind the matrix algebra, as in your code you would be working with matrices and not the single values.
because i checked the same material in 4 different VNA and given different results.
Which difference did you see? as in please explain this point of yours.
Regards.