It might be helpful if you stated as clearly as you can what it is you are trying to do, rather than simply what error you are encountering. If you already said this in a previous thread, then I may have missed it or forgotten.
What is the overall time period you want to model? One day, or multiple days? You can run in 21-h run segments, followed by a 3-h run segment, and then repeat as many times as you like. I’m not clear why you would want to do so.
Your gridded emissions files start at 0Z and contain 25 time steps each. Do you have separate emissions data files for each day?
Your met files start at 040000 on 1 Jan and contain data for 741 hourly time steps, so presumably you want to run for about a month.
Your BNDY_CONC file starts at 030000 on 2 Jan and contains data for 5 6-h time steps.
If you have multiple BNDY_CONC files, then why not put them together into a single file, analogous to what you have done for the met data? You can use m3xtract for this, appending to the existing file as you go, until you have a month-long file.
Then you can start at 0Z on Jan 3, and run for 24-h periods. If you really want to start at 030000 on Jan 2, then first do a 21-h run segment, and pick up the run from there.