I was wondering if the manifold needs to come off or just the throttle body to clean the EGR. Any ideas about what would be best to clean the EGR ports?
If you had gave some information about what kind of car this engine is in I could help you. On most cars the egr valve is mounted to the exhaust and runs into the side of the throttle body. Usually a brass brush and some strong solvent will clean it.
use a tiny mirror on a metal rod to look into the throat of the throttle body. You can see the port on the back of the throttle body throat. You can usually tell if its potentially plugged that way. I don't know of a way other than that to tell.