Hmmm. I think I prefer the version that you originally posted. I like the idea of having to face a choice. (I think that made the appearance of John's father make more *sense* in the scheme of things.) I do think the ending was ambiguous but I had almost thought that it was intentionally so. A Lady and the Tiger ending, really. So I think there were some things that probably did still need to be tweaked a bit to get your conclusion across.

That said, I don't always think that the harder a story is to write, the less you'll like it. (Though, the stories that get done in two hours are often so exhilarating and right.) I think sometimes that's a mark of needing different people to read it, than you'd normally have. (Because, sometimes, a fresh perspective is incredibly important.) But the fact that you're still driven to work on it even when it's hard means that the story itself needs to be written, you know?