Wow! Very impressive!
I don't want to give too much away, obviously, but it sounds like you've pretty much figured almost everything out!
I will say that Dvorak's Humoresque does play a part in the story, but there's a very subtle clue to it hidden at the very end of the game... (It's not too important though.)
And there's a good reason John's name isn't mentioned at the end! (After all, he's a bit different from the others...)
(Also, I'm super impressed you got the final puzzle, and thanks for giving the hints to Aprot!)