You don't ever want to clean your entire pump at once, i usually just use sponge filter media. when i service a pump I do half the pump at a time and just basically wash off the excess residue off in old fishtank water, never do the whole pump at a time and never use tap water always use old fishtank water that you have removed from your tanks. You can wipe out all your beneficial bacteria and kill the cycle in your tank if your not careful and that can cause cloudiness in your water.
Wow, i have seen some algae water blooms but nothing like this lol Id be worried my fish were going to turn green too!
I hope things are better now, sorry i laughed but ive never seen anything like it