How does Kris realize what's going on?

Lemme try and answer to the different questions you have brought up.. and yes, it was as awesome film!

ref - Upstream Color Explained

All off the victims simply live out their lives. Except for Kris and Jeff.

Kris’ pig and Jeff’s pig end up mating on the farm. Let’s be clear about this. The pigs mate first. They are connected to Kris and Jeff telepathically. This leads to Jeff and Kris to have an inexplicable attraction to each other.

The Kris pig gives birth to piglets. The Sampler dumps the piglets and kills them. This causes a chain of events to trigger.

Because of their connection, Jeff reacts violently by punching a coworker and throws his work papers just like the Sampler does. Kris begins to cry inconsolably. Also, Jeff and Kris get into a state of panic and hide in their bathroom inside their bathtub. They are feeling the fear and anger that their respective pigs are feeling.

The death of the piglets triggers something in Kris. But she’s in a dissociated state where she’s not acknowledging even Jeff. All she’s doing is reciting lines from Walden, unknowingly.

So now Kris and Jeff know that there is some connection to Walden. Eventually, Kris is able to see and feel the sampler.

Her agony of the loss of the piglets is so intense that she’s now made a reverse connection to the Sampler. Jeff and Kris go looking again, but this time Kris has an idea what she’s looking for. She’s able to get a vague sense of the area they need to go to. They land upon a location which has a mailbox in the name of Quinoa Valley Rec. Co

When they listen to the music produced by the sampler Kris is able to make a complete reverse connection to the sampler. She is able to locate him because of this and she shoots and kills him. Her ability to see the sampler (mentally) is what is shown in that scene where she looks straight into the eyes of the sampler.

We are shown a scene where Jeff, Kris, and the Sampler sit in a white room with a table and bunch of chairs. Now, this room doesn’t really exist. It is a mental space where the Sampler is able to see Jeff and Kris. Initially, the Sampler looks at Jeff and Kris not knowing what is going on. Right after, Kris looks directly at the Sampler.

That is how she's able eventually put an end to the cycle..

About the rocks.. looks like that is more a coping mechanism to deal with a missing part of your life that has ruined everything for her..

Over the year Jeff and Kris have each developed a repeating habit. Jeff picks up blue coloured candy, and Kris dives to a pool bottom and surfaces rocks. These repeating actions appear to be ways in which they are coping with their respective trauma.