John Crowell
You're asking the right questions. But I believe that there is no original ontologically grounded structure in your model of the Universe.
<<This lowest level consists of large quantities of one substance - that I call C*s - in a state of chaos.>>
The concept of "substance" and "chaos" is not an ontologically based structure.
"The event of grasping the structure means understanding." (G.Gutner "Ontology of Mathematical Discourse")/
Have you ever dealt with the problem of ontological justification / substantiation of mathematics (ontological basification), which means knowledge in general?
See the article by D.Bukin "THE CRISIS OF THE FOUNDATIONS OF MATHEMATICS AS THE CRISIS OF ONTOLOGY"
[http://www.unn.ru/pages/e-library/vestnik_soc/99990201_West_soc_2011_4 (24)/15.pdf]
<<The combination of creative mathematics, creative algorithmic computations and creative intelligence would provide the “tools” for comprehending and explaining a complete, comprehensive and comprehensible world.>>
See the article A.Narignani "Mathematics XXI – a radical paradigm shift. A Model, not an Algorithm"
[http://vphil.ru/index.php?id=255&option=com_content&task=view]
<<Science is the search for truth about the natural world.>>
Could you draw your truth - the physical/metaphysical first-beginning of your model of the universe?
A.Zenkin: "the truth should be drawn..." (SCIENTIFIC COUNTER-REVOLUTION IN MATHEMATICS)
[http://www.ccas.ru/alexzen/papers/ng-02/contr_rev.htm]