Oh, thanks for this, Ghostwhisperer!
I've seen the Chapel Yard gravestone but didn't know about the Drumnadrochit ones. I'm certain that the John Kennedy mentioned is Allan's brother, but I have no evidence. Donalds, Johns and Alexanders abound in our family.
The Allan Kennedy, stationmaster, is, I think, Allan's son Alexander. He pops up in one of the censuses as Allan, but the birth date is the same as Alexander.