On second-viewing can confirm this movie is perfect... what may at first seem loose and meandering is in fact profoundly tight in its narrative construct once you piece together the story.

Spoilers ahead as I give a brief interpretation of the movie.

I adhere to the Gaian interpretation, that what is happening in the story is a consequence of Mother Earth responding to the hubris of modern man. Firstly, what may seem as disparate parts of a process that leads towards the main characters symbiotically-linked with pigs, is in fact ordained by a higher will. Carruth leaves the relationship between the sampler (pig farmer) and the pusher (the extortionist) ambiguous however there is one big tell to indicate there is a common doctrine being followed (and this is not just a organic life finds a way process): both the pusher and the sampler ply Kris with a glass that has a blue marker determining to what level of liquid is meant to be drunk. Something this out of the ordinary cannot be a coincidence. Also, both sides are co-dependent from inception of one another and therefore require a spontaneous mutual act (what is the business model of the pusher without the sampler coming in as cleaner - to leave the victim with worms intact, going to a hospital and exposing the attack? likewise, who does the sampler have to summon without the pusher to do his part?).

Added to this, the sampler is aware of the pusher insofar as there is a brief scene where Kris is at the bank disputing her lack of funds, and sitting beside her is a man who we see a glimpse of profile - there are no other characters this could be, and on a third viewing I could probably confirm the identity. Suffice to say, even if the sampler was not there at the bank for that particular scene, he is cogent of the extortion effects on each of the victims in his pig pen, and while these two members of the process may be estranged somewhat, there are not disparate entirely.

This leaves open the possibility of a higher will in the form of a corporate entity or a divine force. The sampler and pusher could be seen as the fieldwork subsidiaries of a larger covert enterprise (the labeling of the flowers - I forget what it said exactly, something like Exoticas). However I lean towards the interpretation that it is a divine will interceding to get these parts in motion to work to create a desired effect (as the one poster tagline goes: You can force your story's shape, but the color will always bloom upstream). We see this on one tier, with Kris and Jeff as metaphorically downstream of the pig pen, they have some free will but in some fundamental sense they are compelled by activities upstream. What is perhaps less obvious, particularly on one viewing, is that there is another tier to the story, the one that compels the sampler to go into the woods and sample sounds. He too, is downstream, he too is compelled by a higher force. The higher force is the sound, the same one that Kris and Jeff read about in Thoreau's Walden (and which Thoreau as an evangelist testifies too) - in a pivotal scene, Kris finds a yellow plant in the pool and pulls on it, the effect being a ringing of a bell, inter-cut with all the scenes of the sampler making sounds, this while Jeff is reciting the key revelation in Walden, here the equivalence of divine enlightenment, drawn to the source. Soon after, Jeff and Kris listen to the ambient cd of the sampler, and this is their means of finding the sampler, of going upstream, and ultimately killing him. There may be some scientific link with sound and its effect on that particular kind of worm, but regardless it seems to be a natural sound, and Thoreau's seclusion from the maddening crowds, is a parable of returning back to nature, returning back to the fold.

The intent therefore of this sound instructing a process through the intermediary effect of a tapeworm, is that of imposing on mankind a means for them to reacquaint with the holistic experience, and cross-pollinated with another species, experience a sense of connection and empathy with the world that was growing more and more distant and fractured. Upstream Color is the self-correction of the planet, or the ecosystem, where one point diverts too far (shaping its story but not its color) the upstream effect intercedes and ensures the well-being of the whole.

Also you have to ask how does the sampler have the ability to intuit the experiences of the pigs? He probably experimented himself, perhaps the pusher did too, and they are reacting on an intuitive level off of each other… memories bleeding over, blue line on cups and all. That said, they need to be linked by a higher force as they are operating on a different tier from everyone else, as demigods to create the means for revelation (the reciting of Walden being part of the doctrine).

Of course there is a lot more to the story to parse, but this is the main thrust of the story, that I read into it.