Hey OP, not sure what you're on about, but as a condensed matter physicist let me tell [or remind you of] something: the things you have described (abstractions, mental events and "facts", but I couldn't define "facts" precisely in my head) mostly arrive from conciousness. Now, whatever we mean by the word "conciousness", it is actually still undecided if it is a mere effect of atomic configurations, or something else. More specifically, things like conciousness arise statistically through emergence (en.wikipedia.org/wiki/Emergence) and, as you probably know, emergent effects (of which a simple example would be the vortex shape and energy behavior of a hurricane) do not show if you isolate a single element of the system (e.g a subatomic particle).
Of course, you could just tell me this is merely the combination of a configuration of atoms and a process which depends on all of them at once. But, as any physicist knows by heart (and you probably do too), many-body theory is heavily inconsistent - we do not really know if our systems would actually demonstrate the emergent effect if we were able to solve them - we can only do this (solving) with approximations (very bad ones mind you, like summing and subtracting infinities and claiming we did nothing), and our approximations are, invariably, a mere sum of individual processes and configurations, hardly the actual (collective) thing.
Richard Feynman, Stephen Wolfram and others developed amazing methods to deal with systems with emergence, but they never really pinpoint the definite "yeah, this single term here is the emergence" answer. Interactions are an open problem and you'd be dishonest to claim the processes and configurations are everything there is, if you don't even know every process and every configuration to begin with.
Thus, we can't REALLY demonstrate, straight from set theory (much less from the quantum field theory we use to butcher set theory daily), that "all there is" (I had problems thinking of this too, do you mean a universal set of sorts?) only contains subatomic particles and their processes and configurations - for we can't relate these configurations and processes to *causing* emergent effects, we can only guess they always exist together from observation (i.e they merely correlate, at best, we don't know if there's causality chains there).
Nevertheless, I have not fulfilled all of your rules: I am not familiar to contemporary metaphysics. What do people do with that nowadays, and can you recommend some sources?