I had an issue when clipping my data in which the cell size would lose squareness (either the x or y for cell size differed) or I would end up with either one or two extra columns or rows in my data. After going through quite a bit of suggestions from the ArcGIS help forums, I finally found a solution which worked.
If you are using ArcGIS, you will need to have the Spatial Analyst license.
These are the steps I use to produce a series of rasters with the exact same extent and cell size.
1. Open a blank ArcGIS document
2. Set the geographic coordinate system for the data layer to that of your location data (usually WGS1984).
3. Get all your data layers in the same coordinate system that your location data is in (usually WGS1984).
4. Cut all your data to a slightly larger extent than you plan on using for your analysis.
5. Resample all rasters to the cell size of your lowest resolution raster.
6. Cut one of your data layers to a boundary polygon shapefile.
7. Use Extract By Mask (be sure to check the to cut all the remaining raster files.
8. Convert all your new rasters to ASC.
Within ArcGIS 10.4.1 the tools mentioned above can be found in ArcToolbox under Spatial analyist, Data Management, and Conversion folders.