How to add a phase shift to a sin wave in the frequency domain with fft?

You did not make a phase shift.

What you did was to add a 6000-vector, say P, with constant value P(i) = j π to V, the FFT of v.

Let’s write Ṽ = V + P.

Due to linearity of the FFT (and of IFFT), what you have called back_again is

        ṽ = IFFT(Ṽ) = IFFT(V) + IFFT(P) = v + p

where, of course, p = IFFT(P) is the difference values-back_again — now, let’s check what is p…

In [51]: P = np.pi*1j*np.ones(6000) 
    ...: p = np.fft.ifft(P) 
    ...: plt.plot(p.real*10**16, label='real(p)*10**16') 
    ...: plt.plot(p.imag, label='imag(p)') 
    ...: plt.legend();

As you can see, you modified values by adding a real component of ṽ that is essentially numerical noise in the computation of the IFFT (hence no change in the plot, that gives you the real part of back_again) and a single imaginary spike, its height unsurprisingly equal to π, for t=0.

The transform of a constant is a spike at ω=0, the antitransform of a constant (in frequency domain) is a spike at t=0.

On the other hand, if you multiply each FFT term by a constant, you also multiply the time domain signal by the same constant (remember, FFT and IFFT are linear).

To do what you want, you have to remember that a shift in the time domain is just the (circular) convolution of the (periodic) signal with a time-shifted spike, so you have to multiply the FFT of the signal by the FFT of the shifted spike.

Because the Fourier Transform of a Dirac Distribution δ(t-a) is exp(-iωa) you have to multiply each term of the FFT of the signal by a frequency dependent term, exp(-iωa)=cos(ωa)-i·sin(ωa) (Note: of course each one of these multiplicative terms has unit amplitude).

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An Example

Some preliminaries

In [61]: import matplotlib.pyplot as plt 
    ...: import numpy as np                                                                                           
In [62]: def multiple_formatter(x, pos, den=60, number=np.pi, latex=r'pi'): 
             ... # search on SO for an implementation
In [63]: def plot(t, x): 
    ...:     fig, ax = plt.subplots() 
    ...:     ax.plot(t, x) 
    ...:     ax.xaxis.set_major_formatter(plt.FuncFormatter(multiple_formatter)) 
    ...:     ax.xaxis.set_major_locator(plt.MultipleLocator(np.pi / 2)) 
    ...:     ax.xaxis.set_minor_locator(plt.MultipleLocator(np.pi / 4)) 

A function to compute the discrete FT of a Dirac Distribution centered in n for a period N

In [64]: def shift(n, N): 
    ...:     s = np.zeros(N) 
    ...:     s[n] = 1.0 
    ...:     return np.fft.fft(s)                                                                                     

Let’s plot a signal and the shifted signal

In [65]: t = np.arange(4096)*np.pi/1024                                                                               
In [66]: v0 = np.sin(t)                                                                                               
In [67]: v1 = np.sin(t-np.pi/4)                                                                                       
In [68]: f, a = plot(t, v0)                                                                                           
In [69]: a.plot(t, v1, label='shifted by $\pi/4$');                                                                   
In [70]: a.legend();

Now compute the FFT of the correct spike (note that π/4 = (4π)/16), the FFT of the shifted signal, the IFFT of the FFT of the s.s. and finally plot our results

In [71]: S = shift(4096//16-1, 4096)                                                                                  
In [72]: VS = np.fft.fft(v0)*S                                                                                        
In [73]: vs = np.fft.ifft(VS)                                                                                         
In [74]: f, ay = plot(t, v0)                                                                                          
In [75]: ay.plot(t, vs.real, label='shifted in frequency domain');                                                    
In [76]: ay.legend();