I did another test run on the track. Whistle gets slightly louder when I press the "Whistle" button on the transformer, and slightly softer when I press the "Bell" button. I also played with the e-unit switch and discovered that there is indeed a mechanical grating sound, so off the track came the train and tender.
It took me a moment to figure out how to take 611's shell off but figured that out and realized I had no idea what to do. Didn't touch anything, put the shell back on. Photo without shell is attached.
Also attached is a photo of the MSOS board. I don't have a clue what's wrong with it.