Firstly, I would kindly ask why you use such an outdated version of CMAQ…
Secondly, it would be very easy and convenient to use CMAQv5.4 to solve this problem as CMAQ does provide vertical column density for several air pollutants (NO2, SO2, etc.) in CCTM_PHOTDIAG files. The only thing you need to do is to set the PHOTDIAG in the run.cctm.csh file to T if you upgrade the CMAQ version.
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