My suggestion is to create 3 different versions of run_mcip.csh, one for each nested WRF domain.
cp run_mcip.csh run_mcip_d01.csh
cp run_mcip.csh run_mcip_d02.csh
cp run_mcip.csh run_mcip_d03.csh
You would then follow the instructions in the README.md to edit each run_mcip_d01.csh script to specify the input files and GRIDDESC file for that domain, then run mcip for that domain. If that is successful, proceed to editing the run_mcip_d02.csh and run for that domain, and if that is successful, proceed to edit run_cip_d03.csh and run.
Note, this question was added to an old issue under the CMAQ tag, and may have been missed. Please create a new issue, if additional assistance is required and use the MCIP tag.