A) You can save log files by redirecting the output (this is supported in most shells): backrub.linuxgccrelease -option1 -option2 > logfile. The > redirects output to logfile.
Can you attach your resfile and params file?
C) Does your input PDB contain a residue of the adduct type, or a regular cysteine? You can try it both ways. If you name it like the adduct, then the PDB reader should be able to add the extra adduct atoms, even if you give it cysteine as input (be sure to remove HG).
D) It does not matter what folder the new parameters file is in, so long as the path is accurate – the folders themselves are only for organization. It does matter that you put it in the fa_standard residue type set.