A:  I think this has to do with what you think the Third Impact was.  I donot think anyone died, and I donot think that Gendo thought this either (Not sure about Fuyutsuki, but he did know about Gendo's overall plan.  Remember during EoE, he asked if Gendo had met Yui yet)  Gendo was looking to actually cause the Third Impact, most likely to see Yui again (this I'm not too sure of). And (now this is a little bit of speculation) Adam sort of did come in contact with an angel.  In EoE, Adam was imbedded in Gendo's hand, and he stuck his hand into Rei, and was absorbed.  THen things got out of hand, as Rei betrayed him.  I know this isn't a direct answer to your question, but maybe it helps.
 

Q:  After the Third Impact, the only humans shown on Earth are Shinji and Asuka. We see souls still in orbit.  Are we being led to believe that Shinji and Asuka are the only two left on Earth?

A:  This, again, is up to interpretation. Some people say that Asuka was actually a mix of Asuka, Rei, and Misato.  And really, Asuka had already died earlier, so the bandages are unexplained.  Everyone else had been absorbed into the sea of LCL, they had become one existence, but they were still human.  At the end of EoE, we hear Yui talking, remember what she said?  SOmething like about humanity having the ability to heal itself, I don't remember exactly, and will not risk quoting EoE incorrectly.
 
 

Q:  Also, some scenes in episode 25 are directly from EoE, leading us to beliebe that it occured afterwards.  What exactly is happening?

A:  There are two main theories for this, one is that EoE is an alternate ending, which I totally disagree with, and the other is that eps 25 and 26 coincide with EoE, which I do agree with. The last two eps, I think, are more internally about what is going on within Shinji and Misato and such.  EoE is about what is happening physically.
 
 

Q:  I heard that there was an eva that never even showed up in the series, it blew up or something. what happened?

A:  Eva Unit 04, while being manufactured in Nevada, USA, dissapeared along with the entire base it was stationed at.  It didn't neccesarily "blow up", but more of just...vanished.  It was suggested that something similar to a Sea of Dirac, shown earlier in the series, was responsible.
 
 
 

Q:  Misato said that humans were the last angel, is that true?

A: Two possible explanations come to mind.  One:  Misato was just saying this as some type of cryptic insult; and Two:  As we've seen throughout the series, the Angels have been becoming more and more sentient, and independant.  They seem to be evolving right in front of the viewers...culminating as Kaowru Nagisa as the acme of its ascent.  Now, in episode 24, Kaowru says something to Rei like, "You are the same as I."  I don't believe that he was refering directly to her, that she was an Angel, but more that she was a child of Lilith.  But humanity as a whole was also a child of Lilith, and in the end, returned to be with Lilith (Well, until Shinji kinda screwed with that).  And, more to do with the actual question, Misato was, in context, talking about the information she obtained while hacking into Seele.  And Seele's plan was to evolve humanity in a sense.  So maybe, Seele was trying to have humanity obtain the form of an Angel, because the Angels were not based in our form of being.  So in bringing humanity together as one, they would obtain the form of an Angel.  Those are my two best theories.
 
 

Q:  Why did angels want to go to Adam and not Lilith?

A:  Well, supposedly if an Angel came in contact with Adam, the Third Impact would happen.  I'm not too sure about this though.
 
 

Q:    I heard them [Seele] say once that the beginning and the end meet in the same place, so are we led to believe that the world is starting over and that Asuka and Shinji (as we see at the end) are to be Adam and Eve?

A:  Well, first off, we are led to believe a lot of things.  The end is kind of open to interpretation.  I will tell you two  interpretations I have come up with though.  I don't believe that the symbolism is that tangible, in the sense that Shinji and Asuka are Adam and Eve.  First off, everyone else is still alive.  Yui even says that humanity has the potential to return, and that Eva will prove its existence forever.  So then, since humanity is already there, I don't think an Adam and Eve are necessary.  Shinji chose this world, and chose Asuka to be in it.  My second theory, is that the end never happened within the physical world.  Shinji and Asuka became just like the others, with one difference, they were the only two people within an Evangelion unit when Lilith fell.  So they are outside the others, and they are the entire purpose of the Human Instrumentality Project.