Thanks for posting these files.
Looking at the header of the ISAM_REGIONS file you posted as ISAM_REGIONS.txt file, it seems the file does not fully comply with I/O API conventions, leading to an error when CMAQ tries to read from it.
Specifically, since variable names in I/O API have a length of 16 characters (including spaces), the VAR-LIST attribute cannot be " CD CN CB CQ YX YD OT " since it needs to contain 16 characters (including spaces) for each variable and have a length of NVARS x 16. You can look at the headers of MCIP files for examples of properly constructed VAR-LIST attributes. It also appears that a number of the attributes in your file that should be of type integer (FTYPE, GDTYP, NVARS, STIME, SDATE, etc.) are of type real which may also cause problems.
Generally, it is strongly advised to use Fortran code linking in the I/O API libraries or programs from I/O API’s M3tools to create CMAQ input files such as this one to ensure that they comply with I/O API standards. There are a number of other threads discussing this topic: