When I get fosters/rescues that come through our house, I disinfect everything with a dilute bleach solution, then a good wash down to get the bleach off for the next time that I use it. Litter boxes get soaked in bleach water, wicker stuff like hay baskets get dunked in boiling water, cardboard gets tossed and linens go into the wash. If the linens have a lot of pee on them, I’ll put 1/4 cup of white vinegar in the wash to knock down the smell. The tarps and the bottom of the dog pen are the hardest to clean, I usually just wipe them down with a dilute bleach solution, then hose them off in the back yard.
I do not use a formula for the bleach, just pour a couple of capfuls into a bucket of hot water and run with it. Since you are worried about E. cunculi, I do not know if bleach takes them out or not. I am most concerned with Coccidia, because most of our rescues have been in the wild for a while, and most of them pick it up along the way.
Handwashing with hot water and soap should do the trick.