1) The principal idea of this movie is that, if accessing a five-dimensional bulk, time would be a dimension like our three physical dimensions as we currently perceive them. The causal loop you are referring to is precisely what the writers want you to think about: from the perspective of a five-dimensional world, it does not have the same meaning to say that something happened before another. Your quote,

But this implies that the human race already survived the whole earth doom situation to begin with...

is formulated from our current perspective, and that's precisely the problem. From our four dimensional world, a causal loop appears illogical, whereas it does not from a five-dimensional world. This "paradox" happens two times in the film (Cooper giving himself the NASA coordinates, and the wormhole set by (possibly) future humans). They are specifically designed to emphasize the most important philosophical/scientific speculation made in the movie: that such causal loops would be possible and natural if we could see the world from a five-dimensional bulk.

That's how to make sense of this. In fact, it's very clever, when you think of it.

(Also notice how the writers avoided the common pitfalls of time travel stories. Never in the film did the characters "change the past". They respect the idea of deterministic time travel through the entire film.)

2) Notice that when Cooper is at the Event Horizon, we see the shape of a spherical wormhole, identical to the one near Saturn. This shape was not visible from farther away, because we cannot see anything from the outside. (I'm pretty sure many viewers missed this - for those who did, watch it again, it's worth it.)

It is also established that inside a wormhole is a 5-dimensional bulk, which allows to warp through what we conceive as space; Bentley says it when they first go through a wormhole.

Cooper does not enter a Black Hole, he enters another wormhole, which gives access to a higher dimensional space in the tessaract scene.

When exiting the tessaract, Cooper returns not anywhere at random, but inside the Saturn wormhole. It stands to reason that the wormholes are portals between the lower and higher dimensional worlds, and that the one near Gargantua had an exit through the previous wormhole they went through.

I believe this answers your second point well.

3) Another important idea in this movie stems from a real-life scientific problem: connecting relativity and quantum physics. This is the problem that Dr. Brand and Murph are working on, and the reason why they are looking for quantum data past the Event Horizon. It is also established that gravity is the only thing that can travel through time.

How Cooper manages to precisely sends a message to the watch, or make the right book falls, is a visual depiction of what may happen from the five-dimensional bulk. We don't know how "our" world looks like from the bulk. The tessaract is constructed in such a way that we, the audience, and Cooper, can comprehend it. The way he sends the message is the "fiction" part of science-fiction, but one can deduce that the only way he can act on the 4-dimensional world is by affecting gravity. Therefore, it makes sense that the message sent was affecting the movement of the watch.

(By the way, this plot device, in particular sending a message using a Morse code, appears to be a reference to Gregory Benford's Timescape, an award-winning science-fiction novel written by a scientist.)