This is a bit of a stretch, but the knocking might be due to an air pocket introduced when the system was opened up. You might be able to get rid of it by massaging the upper coolant hoses with the engine off and the radiator cap off. This would also be a fitting time flush the entire cooling system, including the engine block, if it wasn't done with the radiator change (probably not).
When you mentioned topping off with coolant and water, two things you might wish to consider in the future: don't use tap water, which could contain certain minerals in it, and instead use distilled water; better yet, use a pre-mix, such as Prestone. These are advanced formulas now, and quite easy to use. just pour in. Generally these are the orange colored formulations nowadays.