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Part of the mystery and excitement about consciousness is that scientists don't know what form the final answer will take.

Part of the basic conundrum of reason
We understand the Universe through reason but
a basic tenet of logic is that a thing can not be used to explain itself
reason cannot explain itself

That's correct, you cannot explain (in western logical
empirical ways) some phenomena by incorporating that same
phenomena in the explanation.

If all(and I mean ALL) of your thoughts, emotions, perceptions,
etc. can be explained by the movements/interactions/"essence"/
emergence of the physical universe how do you know those
thoughts, emotions, and perceptions are in any way TRUE?

If all(and I mean ALL) of your thoughts/emotions/perceptions(TEP) are a product
of the random fluctations of newtonian/quantum physical
processes, then how do you know if your TEPs about the
physical processes themselves are TRUE? If indeed, your TEPs about
the physical processare are CAUSED by the physical processes
themselves, then there can be no such thing as a proof.
You have proven that there is no such thing
as a proof!!! Which is absurd.

Obviously there is something "other" than the physical. Call it
a "soul" or "consciousness" or "being" but it's not
physical and I believe it cannot be explained ever by any
physical process. Unfortunately, that fact will lead some
to believe that there is no such thing as physical reality,
which can get you into trouble while using a flame thrower
to light your cigarette.

a basic tenet of logic is that a thing can not be used to explain itself...reason cannot explain itself

The first is not true (sounds like a misunderstanding of Godel's theorems). The second is not logically true, although reason has certainly not yet explained itself.