Yes, you are right I did watch it in 'C.' Luckily, today I have watched episode zero and episode one in the right order for set 'B.' I'll try it out and see how it may be seeing as it may add in a good twist.
You know what, the more I think about it, the episode that you mentioned here does make a bit of sense to be the last for the season. I mean it fits seeing as she opened a new world or so they say. I think in this order it may seems to give off a bit better sense in a way. As for confusing, the Time Traveling was strange in Episode one of the second season, lol.
That is so funny, I prefer the original Yuki however. I see that some of them have stayed in their original gender but has been given a different appearance such as Mikuru. The guy version of Haruhi looks just like Haruhi with the same personality and large smile. Kyon was given a nice gender change though and some of the new looks are really nice. Thank you :).