1: He failed again. That's the inner Sephiroth telling him this. The one inside of him due to the Jenova cell injected in him as one of Hojo's cloning experiment. Cloud keeps saying he is an ex-SOLDIER, but nope. He failed to get in, and has spent this whole time trying to compensate by acting cool or above himself, even taking Zack's persona no less. "So you failed again" is simply himself having difficulty to cope with being (seeing himself as) a failure. This will go hand in hand again further down the road when a certain event happens in the next parts. You have to keep in mind that this is the first part of the story, and as such, everything isn't self-contained in it. Many plot points will be resolved in later parts.
As for Zack, Aerith is an Ancient who can hear the voice of the planet. When you think she sensed him is precisely the place where Zack died. Will they show his death scene in part 2 or did he survived? We'll have to wait for Part 2 to be sure. My money's on the former, based on a comment by Kitase in the Remake's Ultimania book, but I'll come back to this later.
2 and 3: Why are they intervening? Even Aerith, moments before the party goes inside the portal, says "Who knows?" completely puzzled when Tifa asks WTF they're doing around Shinra's headquarter. Then you see Sephiroth arrives, raises his hand, says "listen", and the Whispers come right away behind him. They call those things Arbiter of Fate, but is it really what they are? At first glance, people think they're working against Sephiroth, to make sure a certain timeline happens, but things are most likely not what they seem. Throughout the entire original game, Sephiroth manipulates Cloud and the party to lead them to him. He keeps talking to Cloud, puts ideas in his brain and toys with his emotions. What is clear, is that he can SEE the future. That's made clear by the multiple visions we get throughout the game. Seeing it and being from it are different things. He can have foreseen events without necessarily having experienced them. He is still, after all, at the Knowlespole pulling the strings. The Whispers are more than likely one of those strings.
The problem with your theory is that you start from a conclusion and work backwards from it looking for details that may fit with it. That's the wrong way to go about it. So many people are doing this right now... You start with the idea that Sephiroth saying that line means it's him from that movie. Is Cloud from AC as well because he said "not interested"? Seriously, WTF?!
And I am not resisting so much as thinking those theories are moronic and stretching to ludicrous limits at best. People are needlessly over-complicating things. I am sure the revelations will be much simpler than any meta-crap so many of you cling to.
Now here's a statement made by Kitase, taken from the Remake's Ultimania book:
"We’re not drastically changing the story and making it into something completely different than the original. Even though it’s a Remake, please assume the story of FF7 will continue as FF7 always has from here on out."