Bagheera wrote:the CI tells us that, after 2I, Adam blew up and his soul "flew off somewhere". After that Seele (somehow) retrieved the soul and stuck it in Kaworu. How did they do this? The very fact that they can do this has staggering implications for the rest of the Eva universe, and it means we can't blow off the soul sucking business since textual evidence tells us it very much does exist in the setting.
And now, my reply:
If you want simple explanations, this might be the wrong show for it!
Adam's soul flying off and being captured is stated to be what happened, so, well, we're stuck with that. As for the second "strange and inexplicable thing...
The creation of Kaworu by CE is strongly hinted at in the show. His day of "birth" is Second Impact; someone called the "donor" is scheduled to have a "contact experiment" with Adam on the day of 2I; as Adam awakens, it's said that genes which 'dived' into her have fused with her physically. The pieces come together fairly easily: the genes that "dived" were the donor's, and the "physical fusion" refers in some way to Kaworu's genesis (whether by sexual recombination or something else entirely).
Supplemental materials seem to be on track with this interpretation. The EoE theatrical booklet says, "It is likely that [Kaworu] was an Angel which had been captured by SEELE in the embryo [literally egg] stage." One of the blurbs on the Eva Chronicle "Tabris" info sheet seems very supportive, as well, from what I've made out at a glance; I suppose I should translate it.
The manga also decided to forego suggestive documentary-type flashbacks and just have Ritsuko lay it out in the open.
Humans tried to return Adam to an egg before the other Angels awoke. The result was Second Impact.
Among the data from your father’s research team that was retrieved just before it happened,
I have heard that there were indications of an attempt to use human genes in some way.
If that was actually done in secret, if the Angel born at that time took human form,
and if the Committee got their hands on it, then according to MAGI everything adds up.
There's no conflict between the manga and anime in this regard. Sadamoto provided with bald exposition what I'd been able to previously piece together. It was a pleasant surprise when this chapter arrived.