Sorry that you find understanding the essay difficult. If there is any suggestions you have or clarifications you find may be necessary, please do not hesitate to express them.
From comments I have received in the past years, I think once the axioms of discreteness and matter are understood, the rest pretty much should follow. The problem some of my readers have been having can be traced back to trying to understand the ideas from within the framework of a theory that uses a completely different axiom set. I'm not saying that this is your case, but when it is, the easiest way to understand the ideas is to try to understand them from within the proposed system and then evaluate it for internal consistency and, later, consistency with observational and experimental data (the data, not the theoretical interpretations of it).
In the case of the essay, it may be that there is not enough space to appropriately expand on some of the key concepts. It is difficult to reach an optimal balance between the amount of concepts and the depth to which they are explored. It is even more difficult here since the ideas found in the essay were based on a much larger work, the first part of which can be found here .
That said, the important thing for me, and the only reason I participated in the contest, was to participate into and initiate discussions.