Hi Mike,
In FLUKA the dpa is not explicitly calculated on the level of the atomic lattice due to the Monte Carlo approach of simulation: the material is fully homogeneous, isotropic and static under irradiation. Above and below particle transport threshold empirical laws and effective parametrizations are used (I refer to https://www.aesj.net/document/pnst002/769-775.pdf if you want more information) to eventually arrive at the dpa value. Setting the PART-THR to such a low value probably adds little extra accuracy at the expense of more required computation time. Setting the threshold to 1 keV should in principle suffice but you can easily check if this makes a difference or not. Be aware that in your input file now you set the momentum cutoff (in GeV/c), not the kinetic energy cutoff (in GeV, see PART-THRes | FLUKA).
The bin sizes indeed correspond to 1 cm^3 each (I corrected a typo in my previous answer) but this does not matter for the USRBIN output: all bins are by default normalized per unit volume so there is no need to again divide by bin volume for analysis.
Cheers,
Andreas