I'd guess the reason why we don't really get to see any stamina problems for Marui is that he normally doesn't move around much. His offensive style has just him standing around and waiting for a ball he can convert, so of course that doesn't significantly drain his stamina. This probably changes when he uses Wonder Castle since that has him covering the entire net. Still, his stamina isn't exactly poor to begin with, it's more like average (it's just worse than that of the other three).
Anyway, on the match as a whole: I think the combination of Wonder Castle and Giant Habu will be troublesome for Shiraishi and Akutsu and I'm not sure how they'd really overcome it head-on. Turning the match into an endurance battle with Marui and forcing Marui/Kite to switch back to the Shukuchihou/Myougi strategy seems like a better idea to me. In that case, I'm pretty confident that Shiraishi could stop Marui from scoring a lot of the time, and Akutsu's entire playstyle seems like a terrible match-up for Kite - we've seen that Shukuchihou can be overcome if you can actually get Kite off balance and Akutsu's tennis should be perfect for that.
In the end I expect Marui/Kite to take the first set, but I don't think Marui can keep up WC throughout the whole match. As a result, Shiraishi/Akutsu are going to take sets two and three in my opinion.