Again, it's late, and my weak excuse for arts will have to wait until tomorrow. I enjoyed this update and it's interesting to see the plot moving in noticeably different directions from before, and it's also neat to speculate about what might remain unchanged in either version. Here's a few thoughts that I had.
"Okay, Hicchan~! It's decided!" Misha puts her hands on her hips as best as she can without leaving her desk. "You suck at sign language, so I'm going to teach you!"
This seems like kind of a... lackluster reason for it to occur, even if he acknowledged that it would probably happen sooner or later. In Shizune's route, he of course learns sign because he wants to talk to Shizune. But here, in fact, Hisao doesn't seem to even particularly get along with Shizune, so it seems a little strange that he has no qualms with the idea of eventually having to learn an entire language just to help with student council activities, when he seems to have no real motivation to do either.
"But won't that mean we'll miss our run with Emi?"
I'm a little confused here, seeing as this scene could logically take place right after the previous one. And even if it is the next day, didn't they just run with Emi in the morning before class, not after it? By the end, you mention them running twice in one day, was that mentioned in one of the previous scenes? Why would they do that?
I don't think I've seen a pink-haired person in my life outside of an anime or two.
Fffff, we went too deep, we went too deep. I mean, I know it's anime, so you don't have to explain, well, anything, but Misha's hair striking him as unnatural--when Hanako's purple or Suzu's bluish-green-thing don't--is kind of hard to rationally accept. Really, if Misha's hair was never specifically said to be dyed, I don't think anyone playing would have thought twice about it--and does anyone in the game really act like it's strange? The only time I can think of is when Akira mentioned she liked the brown better, or something to that effect. Anyway. Talking about anime when writing for an anime-inspired-ish setting is murky territory, though not impossible.
One other thing I noticed is that it felt like there was a little bit of a lack of romance in the second two scenes, at least compared to the way Hisao and Misha were acting when they were last at her thinking spot, and how he almost kissed her at the track. I know that going from "we're in a relationship now" mode to "sitting in class together being students" mode can be awkward, but that's something that should come into play, at least in his thoughts, I think. The last scene addressed this a bit, with his thoughts during the staring contest, and I particularly enjoyed the coin toss--Hisao's choice to lie, and Misha's subdued reaction were both intriguing. Still, I feel like the romance--or lack thereof--should have been a little more on the front of his mind, but maybe that's just me.
Edit:
Well that took longer than expected.