It took me days to read this, but I finally finished! This was amazing. I loved your ideas that Snape was trapped in the castle as punishment -- one really does have to wonder what went on during that year of hell of Harry's would-be seventh year. And Severus was such a consummate spy that I had no trouble believing that he'd even fooled the castle. I also loved the genuinely caring relationship Severus and Harry had for each other. It made each bout of their depression, anger, despair, and even "good day" moments so much more poignant.
I'm so glad to see Harry managed to get the castle to free Severus at the end. Imagine the possibility ahead of them -- an actual future! :D