Regarding PMFINE, you are correct that the CMAQ code for the inline dust and sea spray emission streams generates emission surrogates PMFINE_#### which are then mapped to CMAQ model species according to the rules in that section of the EmissCtrl file.
However, the PMFINE (not PMFINE_###) emission surrogates reported in your log file occurred in the GR1 and PT_NONEGU emission streams, i.e. the emission files you prepared offline. Since there are no rules in EmissCtrl to map this PMFINE surrogate to any CMAQ species, the mass associated with its emissions would not be accounted for in the CMAQ simulations. As noted in my previous post, if these PMFINE emissions in your emission input file represent mass that you want to include in your CMAQ simulations, you either need to trace your way back through your emission processing and speciate them into emission surrogates actually present in the EmissCtrl file, or you need to decide “manually” which CMAQ model species you would like to map these emissions to and add a corresponding line to the EmissCtrl file.