I am performing another test with CMAQ v5.3.1 (the WRF settings were left unchanged) which I left the script like that:
set NZ = 23
##setenv CTM_EMLAYS 20
setenv CTM_PT3DEMIS Y
setenv CONC_BLEV_ELEV “1 1”
setenv ACONC_BLEV_ELEV “1 1”
setenv APMDIAG_BLEV_ELEV “1 1”
setenv N_EMIS_GR 1
set EMISfile = emissions.ncf
setenv GR_EMIS_LAB_001 GRIDDED_EMIS
setenv N_EMIS_PT 0
Following what I have read in this topic CCTM emission module