cleaning isn't really needed on the N52 because it still uses port injection, and the intake ports/valves are bathed in gasoline, keeping them clean. When I did the manifold swap on my car with about 75,000 miles, the intake ports and valves were spotless.
but, if you really want to do it, feel free. it's kinda a PITA tho. removing the cover and airbox is only the tip of the iceberg for a manifold R&R.