So how does all this allow for them to have reached any sort of intimacy before the very end of CCS? What exactly is going on between the two during the course of the series? Obviously, they're in love, and obviously, by the end they're a couple. But how does it happen? How do all the clues and hints fit together? Was it really all just long wistful looks and inadvertent touching until the end? And if so, how did passionate Touya, who was obviously aching to be with Yuki since the beginning, hold it in for so long?
The when and how are never actually made clear in the series... unless you're willing to accept that someone like Touya would be content with simply telling the confused object of his affection and desire that he's happy to have him by his side. Don't get me wrong, this is very sweet. But would Touya have let the moment go at that? I don't think so.
This of course, is all speculation on my part... I think that Yukito was not that clueless, and don't think that Touya swallowed his feelings for so long. I don't think it's possible for a CLAMP story to be that simple, I think that with them, it's always what's beneath the surface that counts. I think that the hints of intimacy at the beginning of the series are too strong to be denied. Touya starts to activelly hint about his feelings at the end of the Clow Cards arc. So it's safe to say that by then he'd accepted that he loved Yuki, but was proceeding with caution, so as not to freak out Yuki or jeopardize their friendship. Well, if he was starting to subtly tell him how he felt, what's to say he hadn't gone even further in physically showing him how he felt? This would account for everything I talked about in body language. Not only that, since Yukito obviously didn't reject his advances, it's very possible that it might have gone further at some point than we were ever shown in the "official" story. Specifically, maybe one of those long nights they spent together studying, Touya decided to act on his feelings (whether he might have gone for more than kissing, is of course, a matter of pure speculation ^.~). Yukito wouldn't have pushed him away, he loved him, he wanted Touya just as much as Touya wanted him. But he would have remained unsure of Touya's feelings, because Touya was still reluctant to tell him he loved him at this point, both because he was being cautious and because he wasn't really over his own issues with intimacy, not yet.
And so, Touya and Yukito would have moved their relationship up a notch... into the nebulous space between love and friendship. Never really admitting what was happening, always a little afraid that speaking up would shatter their bubble, they would nevertheless have grown closer, while their relationship grew and evolved until, finally, the silence became too much too bear.
Incidently, Last of all, think about this: when Touya puts his hand on that tree that Yuki is standing agaisnt, and leans very close while starting, once again, his attempt at confession, Yuki's eyes widen in surprise. Surprise at what? At the way Touya is behaving? Or at what he's about to say? This is hardly the first time Touya has behaved in a way that seems more suited to a couple than to a couple of friends (although it is the most aggresive he's ever been). If my specualtion were true, then Yukito would probably be in a state of near shock and amazement at the prospect of finally hearing what he longed to hear from Touya. Not only that... he'd probably be afarid to believe that it was finally really happening.
Again, this is just my opinion, of course. ^.~