Good Stuff.
I like your Evangelion Spoofs almost as much as I liked the TV series & Movies. You're right though about some of the stuff not making, like how did Asuka escape and wind up on the beach beside Shinji, all bandaged up too. Maybe Lillith/Rei did that.
As for the ending, my personal interpetation is that Asuka and Shinji are alive to become the parents of the new human race. Either that or they were the *original parents* and the Earth is caught in one of the those weird time loops.
Anyways, Keep up the goood work.