The electron-phonon couplings (Huang-Rhys factors) are calculated from the reduced frequencies and the displacement vectors connecting the normal modes between the two states.
See http://www.scm.com/Doc/Doc2014/ADF/ADFUsersGuide/page171.html
Try look at some papers from Jeffery Reimers from Sydney University. It's along the line of Dashinsky rotation (sorry, spelling might not be correct). He had a software to do this sort of calculation, which required output file from Gaussian. If you email him he will give a copy to you.
Basically you need to consider the deformation of a molecule along the normal mode coordinates when you put a charge in/take a charge out from the molecule. The tricky bit is how to convert between cartesian and internal coordinates (which, there are papers, e.g. from Axel Becke who talk about this).