The mrggrid program which is part of the SMOKE system is typically used for this, although not sure why you are still using such an old version of CMAQ.
The sector merge scripts in the EPA platforms do this merging, although it is a bit more complicated as the scripts consider representative days and the like. You can find some recent EPA-released platforms here:
In particular if you go to one of the platforms and look in the scripts zip file on the FTP site, you will see the in the SMOKE core the sector merge scripts and the sectorlist file that the script uses.
This may be overkill for what you need. I believe the SMOKE modeling platform Wiki has some information on this step as well.