FFT analysis of summed signal in LTSpice
When you open the FFT dialog, highlight I(L1), I(L2), I(L3). You may want to set other FFT parameters, such as window type.
When you click OK, you are given the option of Alt-double clicking.
Do so and enter the sum of the currents: I(L1)+I(L2)+I(L3)
You now have the FFT of the sum of your currents.
Your FFT plots will benefit (lower noise floor) by disabling data compression (.option plotwinsize=0) 
and reducing the maximum time step in the .tran statement.