Dear Madam,
Your essay is poetry written in prose format. We wish you could have used a gender neutral format like 'it' because there is no bare charge or bare mass. Every perceivable information / object is composite with positive (male) charge in the center (central like bone) confined by negative charge (female exterior like flesh) with both protecting each other differently. Their net internal dynamics makes them male or female (if one extra y chromosome, then male; if in pairs, female. If moves out, positive; if moves in, negative). Human consciousness might have "a non-physical component", but it is revealed only through a physical body. Reality or existence is whatever has a limited structure that evolves in time and is perceivable / measurable directly or indirectly, is intelligible (perceivable or knowable as the result of measurement) and communicable universally (describable in a language as defined in our essay: Transposition of information to another system's CPU or mind by signals or sounds using energy. The transposition may relate to a fixed object/information. It can be used in different domains and different contexts or require modifications in prescribed manner depending upon the context). Thus, wittingly or otherwise, you have included reality in your discussion - "not a follower of the shut-up-and-calculate doctrine".
A model can explain reality, but can we be sure that it fully explains it, particularly when manipulations of its theory-laden characters are influenced by the thinking of the scientist, which in turn are influenced by the social factors - spirit of the age! Reductionism has its own limitations. There is a story about six blind men, who went to see an elephant. Each touched only one part of the creature - leg, trunk, ear, belly, tooth, tail - and described the elephant by that experience only. Though all their descriptions are valid, one who has not seen an elephant cannot make any sense out of their combined statements. The Universe does not duplicate itself. Though all quarks look same and cannot be distinguished from each other, they are different. When you stretch a quark too much, it gives rise to another quark by drawing material from the environment. It does not 'become two'. Thus, you have rightly pointed out that "it also must contain a prescription to identify the mathematical structure with observation".
While science without technology is lame, technology without science is blind. With over-emphasis on the effectiveness of technology, its 'blindness' is increasing, which is manifest in various social and environmental problems. A very large number of people enjoy a cozy life in pursuing and teaching nothingness or self-destruction. We may enjoy temporarily, but ultimately everyone is going to suffer. We have discussed these subjects elaborately in our essay. You are welcome to read it because of many similarities.