Ayanami-sama and Cirus were solidified as a couple in my own mind, so the scene between them from here on out have a certain assumption of familiarity, which is played on when Rei wakes Cirus up to take his own usual anxiety of being caught in a delicate position into account. In turn, Cirus is more accepting of the fact that she cares for him, too, and so his anxiety is diminished. Now the characters grow in relation to each other, not just stand-alone characters (not to say that Ayanami-sama couldn't stand alone for an entire series, just stating the fact of Kenosis... myarf.)

Cirus stroking Rei's back does seem a bit of a stretch for his character, but with the innocent intimacy dynamic created between them, he's just giving her comfort (and he'd whip his hand back if she so much as blinked in a manner that implied she didn't like it.) Effectively, he's more aware of her 'unsaid permission' than before. Rei responds by pulling back into a dozing snuggle, which I enjoy so much. So cute.

Getting things back under way in classic style, Misato cuts in and uses her insinuating humor to get Cirus riled up immediately. No, they weren't naughty, but Cirus is well aware of how likely that is in the situation he'd wound up in with Rei. With the invitation to breakfast, and Cirus catching himself admiring Rei's adorable hair-toss with her affirmation, they head to get dressed and enjoy breakfast.

The finishing section, breakfast, is just intended as a nice, easy transition from the first story to the second, and since the two are now fused, it's just a lovely fluff-scene with some character interaction. In Kenosis, a tactic I enjoy to use to finish a scene is often a line of dialogue that's definitive and lends itself to moving on. Using Misato's little joke at Cirus about 'showing off', and Shinji's offended sensibilities, it presented a splendid transitional dialogue line from Misato herself, allowing the next chapter to start off smoothly.