Thanks for all of the responses.
I'm personally leaning towards the flywheel idea. The sound frequency increases with speed just like it could be something getting caught on the flywheel. The sound does seem to have no performance issues with the locomotive. My biggest fear is that I am going to cause expensive damage to an expensive locomotive.
As I'm sure is the case for everyone here, I want to be spending money expanding my railroad empire rather than fixing things that I already own.
One more question... I won't void my MTH warranty by opening up the locomotive will I? It would be just to check if nothing is getting caught.
-Marc