If you used the MCIP version that came with CMAQ5.4, you need to define the LUFRAC_CRO variable in your run script to point to your LUFRAC_CRO_* file, along with defining the other variables pointing to the MCIP output files.
To do so, change this line
#setenv LUFRAC_CRO $METpath/LUFRAC_CRO.$GRID_NAME.${NZ}L.$YYMMDD
in run_cctm_2010_4CALIF1.csh to
setenv LUFRAC_CRO $METpath/LUFRAC_CRO_${APPL}.nc
analogous to the setting for the other MCIP output files in this example CCTM run script.