Bob has now updated the program so you can specify the number of points to match; by default, it will still zeropad up to a "fast" number as before.
In your case with 112 points in the time series, running:
3dDFT -prefix AAA FILE
... would give you an FFT zeropadded to N=120 points.
Now, with the newest version of AFNI, you could run the following:
3dDFT -nfft 112 -prefix BBB FILE
... and that will process (more slowly) with 112 points.
The latter should land you on your frequency more directly, if that's what you want.
Re. the phase calculation:
Ah, I didn't see that you had included "-cx2r PHASE" in your 3dcalc command, OK. Sorry for my confusion.
--pt