Do parasites mainly affect the intestines?

Many areas. Parasites are usually ingested so intestines are usually the first area to be affected. However, some parasites can migrate to the liver, brain, muscle, skin, lungs, heart, and many other areas.
Some. Ascaris also goes to the lungs, malaria to blood and liver, larva migrans to the skin and other organs including eye, tapeworms can end up in the brain, and schistostoma live in the bladder.