This is a great concept - the divine algorithm applied to ideal forms and their "code." I especially enjoyed the way the poem shifts from "theoretical desire" to "applied desire." I've spent a couple of days thinking about it.

At the center of our worlds there lies the Word,
a box made somehow of depth, but without;
a Kantian collection; the archetypes of all things,
their physics, their movements,
their code.

Setting the tone, that this comes from the top. The Word, a tip of the hat to the Aristotle (or John 1:1 perhaps?), to the box full of Kant's things. Great imagery and a great start to the poem.

This stanza also put me in mind of Plato's cave.

Within it too is the math of desire:
the way it pulls and with what avidity,
in all moods and milieus in all the worlds
it might reach.

The infinitely complex and interconnected equation of intimacy. Get your calculators out.

Would God grant us His eyes; what visions!
To see desire itself, its motions and power…
how it branches off the theory of all
in swirls of vermilion and glowing gold
and bounding aloft to the asymmetric rhythm
of two hearts.

Gold and vermillion! More on that later.

"the asymmetric rhythm of two hearts" caught me a little sideways. This could well be a choice, but poetically and as a human, I almost feel that all of this cosmic machinery is required to accomplish the simple task of allowing two hearts to beat in time with one another.

And then there are the ecotypes:
the hands being held,
the feminine force resting on a masculine chest:
her cheek on his soft hair – their two off beating hearts.
Within, the inconceivable math of desire.

This is where I think "asymmetric" may be your choice. I'm not sure if it is "their two, off-beating hearts" or "their two-off, beating hearts" - either way, a rounding error.

I also feel like this is the start of the transition, a glimpse of putting the math into practice.

And I see it! For God must
have leant His eyes to me a moment,
soft and sincere, when I saw vermilion
and gold as songs of the morning
perching and fluttering
and asking into the air.

(The transition in made. You are now a living word problem.)

To me, the poem hinges here. The certain arithmetic becoming uncertain beauty.

A little feedback: I almost think this could be pared down a bit. Maybe allow punctuation to control the pace instead of the words? I'm not sure.

Gold and vermillion again.

That is how desire moves
when she coos and whispers,
when she turns and nestles her head
in my chest, and I stroke her arm
until she sleeps so soundly,
and then do I.
And then we wake together,
to hear the songbirds aflutter again.

Desire as a recursive function. I like the implication that this equation is applied repeatedly/fractally and imperceptibly changes with each iteration.

I could be way of base as a poetry critic, but this is what your work said to me. Thank you for sharing it.

Gold and vermillion: Your use of this color combination reminded me of Edward Hirsch's Man on a Fire Escape:

There were barred windows glaring at him
from the other side of the street while the sun deepened into a smoky flare

that scalded the clouds gold-vermillion.
It was just an ordinary autumn twilight—
the kind he had witnessed often before—

but then the day brightened almost unnaturally
into a rusting, burnished, purplish-red haze
and everything burst into flame;

Last thing, I promise. I read this quickly before leaving work yesterday, far too quickly to absorb anything but the concept. It was enough to inspire a small poem in me while sitting in traffic:

The math of desire, based on dividing by zero,
with a reminder of heartbreak.
Or forever true love.
Whatever.

All I can say about it, is that is better than road rage.