Betty's eating disorder and maybe had a flashback to Don's life with Anna? 

I reckon the bodies are real. They're not the Stark boys, though, but the two orphans that were sent to the farmstead.

Fucking stupid ending. The final few episodes were very ropey compared to the extremely high standard of the previous 3 and a half seasons. The ending was a complete cop-out from a story-telling point of view. So little resolution! Ronald D. Moore explained in a podcast that the writers were struggling to tie up the loose ends and have a properly satisfying ending – he decided to make it about the characters instead of the story. Hence so much silly wankery in the final stages. 
That final, final segment in the modern day earth made me want to kick the TV in.
I can't remember if I checked it myself, but I believe the intro from the last few episodes drops the "And they have a plan" bit. Because hey – it turns out they were just making it up as they went along the whole fucking time.