I highly recommend using Python (along with SR matrices) for handling inmap-related tasks, as it offers flexibility and useful tools to adjust what you need. For instance, you can easily set the coordinate reference system of a GeoDataFrame (e.g., gdf.crs) or work with NCF files using the netCDF4 library. Just make sure that for whatever geographical region you have emissions data, you specify the projection to a two-dimensional space, with an ellipsoid defining the same space—Lambert Conformal Conic Projection can be helpful for this.
I hope this helps! Sorry for the high-level answer, but feel free to reach out again if you’re still facing challenges, and I can provide more details once I wrap up my current tasks.