You can try the R package eixport, with wrf_put
# Read the array emissions,
CO <- wrf_get(file = "Path_to_WRFCHEMI", name = "E_CO")
# Change the values, here you should use your data
CO = rnorm(length(CO))
# Inyect your emissions into the wrfchemi
wrf_put(file = "Path_to_WRFCHEMI", name = "E_CO", POL = CO)
How to deal with the speciation (...