Welcome to the forum. I suspect that you haven't received an answer yet partly because we prioritize assisting students with high-school projects (designed to experimentally test falsifiable hypotheses), and partly because what you seem to be asking could easily veer off into philosophy of science, which is a fascinating area but not something on which many (if any) of us are authorities.
However, I think that the area of science that most directly addresses these concepts is cosmology. When we observe light that has traveled a very long distance, it is a record of events that occurred a very long time ago (you might find it interesting to look up 'light cone'). This is true on a small scale, too, so at some point we are taking it on faith that we can string together observations made at different times and build a theory of science based on all of them. This is reasonable since things are highly consistent, but if you really want to question it, that's where philosophy of science comes in. (Some philosophical-ish questions about perception are starting to come within the experimental realm of neurology, cognitive science, etc, but probably not what you are talking about.)http://en.wikipedia.org/wiki/Physical_cosmology
As for the "sum of the matter/energy in any given 'now'" -- I am not sure exactly what you are asking because the sentence structure has gotten pretty complicated here. But 'dark matter' should be an interesting concept to read about.
I think you might like this book, or perhaps others by the same author: http://www.amazon.com/Fabric-Cosmos-Spa ... d_bbs_sr_2
Hope that helps with your thoughts about this -- it's certainly not a simple topic!