Hi Mekawy,
Thanks for sending along the namelist files. I checked your namelist files but I don't see any issues with the settings though I have a few suggestions for you to consider:
1) Your namelist.input file is named as namelist.iinput (i.e., with an extra "i"). In your run directory, please make sure that the file is named as namelist.input.
2) Your AGGFACTRT = 12 in the hydro.namelist file, which means that for your Domain 2 at 3-km resolution, your terrain routing grid needs to be 250 m (3000/12 = 250). Please make sure that your Fulldom_hires.nc file has a resolution of 250 m.
3) Your namelist.iinput also has an entry for chemistry with dust only option (chem_opt = 401). I guess that you will need to make sure that your WRF runs with this chemistry option before turning on the hydro option.
Thanks,
Yongxin