Sarah did say that she loves him, right (or maybe I'm imagining things?)? And she did tell Chuck to kiss her after he told her their story? She loves him, she wants to be with him, and Chuck obviously loves her and wants to be with her; so that means they are together again, right? As for her memories, I said kind of, so there.
Mel, I'd like to hear what you have to say about that; why it is obvious they are together and would remain so.
For the reasons you stated above, plus the fact that they're soulmates, as we've known for the last 5 years. The final shot of them making out on the beach that held such significance was a pretty good clue, too.
Sarah seemed more like her real self, her seasons 4 and 5 self, by that point, too. She'd already started regaining her memories and who knows? Maybe that kiss was all it took. Chuck is a pretty good kisser.