The interaction between Cirus and Shinji is more unique. We see a harsher side of Cirus, more blunt, and cryptic. It's safe to say Cirus was quite annoyed Shinji noticed. Not so much that Shinji noticed, but that anyone did. The punch of the wall with the closing door shows that Cirus is not quite the cold character we might have thought before. You can probably bet the reason Cirus is so abrupt is my own dislike of Shinji. I find the boy aggravating to no end...
The brief section in the kitchen with Misato is more a natural character-interaction, and excuse to show some character for Shinji himself. Plus, any chance to end on an artistic sentence is fun *chuckles*. And just for fun, yes, Misato was hoping her departure would spur Shinji into speaking, but she knew better than to press the matter.
Possibly the strangest interaction in the entire story. What the reader sees here is the combination of Rei's strange intuition, her confusion as Cirus' behavior, and Cirus' own extreme reaction to the presence of women, but especially Rei herself. Rei is not so much interested in Cirus, as she is puzzled by his behavior. A similar tangent to the one that made her ask 'Do you not have faith in your father's work?' of Shinji on the escalator. She is curious... at least about things that are outside her experience. But no, I don't mean to imply peculiar regard for Cirus on her part. Now the part with Asuka is actually subtly hinting at Cirus' curious penchant to appear behind someone faster than would seem natural. Can he ran faster than normal? Is the person just not noticing? I leave this aspect mysterious. Cirus, of anyone, knew how a woman with a crush thinks, and he wanted to cut any jealousy off at the head... if at all possible.
And again, the reader sees Cirus coming more out of his shell. In scenes like these, I try to have a character suggest something the audience would think of if they were watching a movie, but never get a reason why. Cirus just happens to come off like a jerk at the same time. The scenario that follows is full of 'plot convenience'. The haywire happens to be Rei's Eva, only Unit 14 has built-in swords that are ready so fast, and for some reason, Unit 00's power-jack was jammed. It helps pick up the real story-arc (Cirus and Rei) a little, establishing a true peculiarity to Cirus' regard for Rei (though vice versa is still very much doubted). Gendo's reaction might be heavy-handed, but I had him wanting Cirus gone, so moving at Unit 00 with a huge blade seemed as good a chance to try and catch Cirus as any from Gendo's perspective.
The quick chat between Gendo and Rei makes the point I mentioned above quite clear. Rei is Gendo's pet-project (with about the same emotional investment as the name implies...), so the fear that SEELE is after Rei using Cirus is his main concern at this point. I did, however, use the scene as an excuse to show that Rei feels comfortable around Cirus, as much as she does with anyone. Cirus has my own anxious nature, so his coming up to Rei and checking with her seemed natural to me. It also shows he learned his lessons from the previous interactions, avoiding all unnecessary interaction. Yeah, Rei noticed. Asuka, of course, did also, proving that even the best efforts to the contrary won't stop some jealousy flaring up, but since she still has Kaji, hers will be slow to manifest.