Gendo and Fuyutsuki's talk about a real evangelion and what not made me think the real unit 1 (from the original series/eoe - yes i know sequel talk again!) is actually in unit 06 and not in 08. Unless the translation i read quoted was wrong - they explicitly say mark/(unit?) 06.
This then brings it down for Gendo to use as he wants, as it has now been awoken.
To quote Legandary:
Gendo: The true Evangelion...
Gendo: Its completion will be ushered in by the current body containing Unit-01.
Fuyutsuki: The Mark-06, isn't it?
Fuyutsuki: This means what they are trying to create is not a false god, but a true god at last?
Gendo: Yes. We must hasten the awakening of Unit-01.
Bit of a fan-wank, and probably has holes in it i'm unaware of due to me being rusty in all things eva, but it seems quite convenient to me!
*edited for clarification, quote inserted.