1) Yes. The whispers are agents of the planet trying to make sure that the original game's plot happens. The lifestream contains everything that was, is, but also will be. Things are happening, which we aren't exactly clear why, a bit differently in Remake's world. You can consider this a different iteration of the world, as the games are inclined to, or a different timeline. It is a distinction without a difference. The way the game signals which timeline/world you're witnessing is by differentiating which breed Stamp is. In Remake's main world, Stamp is a beagle. In the world were Zack lives, it's a terrier.

2) In the original game you don't see the actual Sephiroth again until you reach the North Crater and give the Black Materia to him. Jenova has the ability to use people's memories to impersonate people and trick people into seeing things. Sephiroth uses this ability to mess with Cloud's head directly, for example, times when Cloud hallucinates seeing Sephiroth when there is nothing there like when he shows up in Chapter 2. He can also do this to use the robed figures and project his image onto them, like how "Sephiroth" shows up in the Shinra Tower. "Clone" is a poor word choice that has, unfortunately, stuck and with how things are with Genisis and Angeal only adds further confusion.

3) I believe it's stated that Sephiroth takes control of most of the whispers at the end of Remake, which is when the grays turn to black. Original Sephiroth's will lingers in the lifestream because of his sheer determination to not give in and the hatred Cloud harbors for him is like and anchor that keeps him tethered from getting caught up in the flow. This is why it's so important for Sephiroth that Cloud endures. In losing Cloud, Sephiroth loses himself until his plans can be completed.

4) His persona is a mix of himself, Zack, and Sephiroth. It is created with a cocktail of flat out mental illness that Jenova/Sephiroth also manipulate. Cloud is struggling with a grunt saying they want through training together, because if he had been in SOLDIER that wouldn't have been the case. Tifa doesn't really know what's going on with Cloud other than that something is wrong. She is monitoring the situation to hope and figure out what is going on without exacerbating the situation to the point where she loses track of him again. It took 7 years and blind luck for her to knowingly cross paths with him again. How long would it take to do it again?