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I hope you still need an answer
The phase needs mapping. I suggest that you look at https://www.jpier.org/PIERM/pierm16/09.10101003.pdf equation 7, which explains the mapping
to run you matlab code, replace your last line with these three
phi1p=acos((0:Npoints/2-1)/d/Npoints)...
rf transformer nonideal
assuming you would like to create a 4 port trasfromer model
run the simulator with Vg connected to ground, or use your 5X5 s-par model with Vg connected to ground
you now have a 4 port s-parameter block.
build your best estimated trasformer model, with parasitics, etc...
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