Reflecting negative frequency to positive frequency
You could use another approach: allow negative frequencies, do a complex IFFT, discard the imaginary parts of the time domain samples, and multiply the result by 2.
Let's try it in Octave (MATLAB clone) with a motif $[1 + 2i, 3 + 4i, 5 + 6i, 7 + 8i]$ shifted so that its leftmost bin ($1 + 2i$) lands on a negative frequency. FFT length is 8. (I rewrote the results for readability.)

&gt; g = [3 + 4i, 5 + 6i, 7 + 8i, 0, 0, 0, 0, 1 + 2i]
g =

   3 + 4i   5 + 6i   7 + 8i   0 + 0i   0 + 0i   0 + 0i   0 + 0i   1 + 2i

&gt; y = real(ifft(g))*2
y =

   4.00000  -0.89645  -2.00000   0.98223   1.00000  -1.60355   0.00000   4.51777

&gt; fft(y)
ans =

   6 + 0i   6 + 4i   7 + 8i   0 + 0i   0 + 0i   0 + 0i   7 - 8i   6 - 4i


The same time-domain signal $y$ can be generated by synthesizing the first 5 bins of $\text{fft}(y)$ and feeding them to real IFFT (which I assume you use). The 3 remaining negative-frequency bins the IFFT kind of generates internally. You can follow these steps for the synthesis:

1) For each bin of the shifted motif that lands on a positive-frequency bin, copy the value verbatim. (You are already doing this)

2) For a bin of the shifted motif that lands on the 0 Hz bin, double its real part and write that to the 0 Hz bin, discarding the imaginary part, like $3 + 4i \rightarrow 6 + 0i$ in the example. (You are already doing this)

3) For each bin of the shifted motif that lands on a negative-frequency bin, add its complex conjugate (same real part, sign of imaginary part flipped) to the positive-frequency bin that is at the same distance from the 0 Hz bin. This will be one of the bins already written to in step 1. In the second bin of the example $5+6i$ and $\text{conj}(1 + 2i) = 1 - 2i$ were summed to get $6 + 4i$. Don't expect the imaginary parts to cancel, because even if the motif might be symmetrical, those two motif bins are not located symmetrically on the opposite sides of the motif, unless you are synthesizing a 0 Hz sinusoid. It is perfectly fine if the imaginary part remains non-zero; frequency domain bins can have complex values and still yield real-valued time-domain data. 

Oh, and if the shifted motif reaches the Nyquist bin (corresponding to half the sampling frequency) or beyond, do exactly the same things there, mirroring around the Nyquist bin.