I am not sure about your R code or your snippet of data. However, you could do an ncdump on the file and direct the output to text to get it "from the horses mouth" so to speak.
In general, the lat/long export of the WRF grid will not have a linear pattern. WRF uses a spatially projected grid, likely an equal area lambert method or something similar. The ...
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 (...