An XR WILL NOT make a "rattling clacking" noise when assembled properly. They are more noisy than a standard Bravo I, but not rattling or clacking. Also a drive should never be shifted into gear on the trailer with the prop on. Does it make the noise when it is in the water and there is a load against the prop? Does it make the noise on the trailer without the prop on?
My first guess was also internal exhaust flappers. If it's not, then take it to a ceritified Mercruiser shop and let them find the problem.
The boat is always run in the water....Maybe trailered once a year therefore I'm limited to Marine shops located on the lake. No exhaust flappers.....boat has two gatlin mufflers with exhaust ported out the SIDES of the hull. That makes it much quieter down buy the drive so you can really tell where the sound is comin from .It does make noise in the water with a load but seems to go away when engine hits around 1500rpm..