Gear Misalignment almost always excites second order or higher GMF harmonics which are sidebanded at running speed.
The FFT spectrum will often only show a small amplitude 1x GMF, but much higher levels at 2x or 3x GMF. Important to set the Fmax high enough to capture at least 2 GMF (standard practive is for FMax of 3.5 x GMF) harmonics if the transducer has the capability.
Observe the sounds around the unit, if you can hear a modulation e. g. (simply put)the sound varies at a set and repeatable rate you will likely be able to observe this modulation in the timewave form which will relate to sidebands in your FFT spectrum.
If you have access to the appropriate equipment I suggest you perform phase analysis which will be of great help as it is a very powerful diagnostic tool.
I suggest you check for the presence of sidebands, this will point you in the direction of the problem gear as the sideband spacing will be at the rotating speed of the "offending" gear.
This might not solve you problem but give you something to work with, good luck.