I want to clean my system with water before putting anti-freeze in.

If you put water into your system which is mainly steel, when you drain the system it will corrode on the surface.  The glycolated water will then remove this thin layer of rust and sludge will form.  The quantity of sludge will be directly proportional to the size of the system.  When cleaning with water, it is important that the time between draining the water and filling back up with glycolated water is as short as possible.  If you need to leave the system with water in it for several days or leave it in the open air for cleaning, ensure you mount a by-pass filter to remove the oxides that the glycolated water will inevitably remove.