1) In 1996, during a get-together with his old co-workers from his university's branch of the Human Genome Project. His old boss drunkly confesses to him that the massive injection of funding that the Herod Corporation had given to build Naoko Akagi's gene sequencing super-computer had actually come from a group called 'SEELE'. An organization, Gendo learned, that was keen on pushing the boundaries of genetics and metaphysical biology.

2) 'Shinji' was the name of an old schoolmate from junior high. 'Rei' he just liked the sound of.

3) He didn't have any objection to adopting Yui's surname. Her family was of much higher status that his, she was her line's last survivor while he had two brothers with families of their own, and he would do anything to make her happy.