I Know you're looking for the ONE cause for the problem noise...........
(Is this kinked copper pipe it?......I don't think so.....)
I think you need to do a combination of ALL the fixes..........
When the Plumbing supply house is OPEN you need to replace ALL the faucet washers......All the toilet fill valves.......Clean any debris from the lines........open an access hole in the closet and (re)attach those pipes....
Have you checked for excessive water pressure.......