I should start this by saying that I'm not a scientist or a linguist. I
don't know that this will be of any help in deciphering the Mystery. It
seems to me, though, that much of the information contained in the
newspaper texts and in your correspndence with The Orphanage is
applicable to the field of Alchemy. Several of the names that show up
with regularity have some sort of connection with Alchemy. Martin Luther 
is quoted as saying

 "The science of alchymy I like very well, and indeed, 'tis the
philosophy of the ancients. I like it not only for the profits it brings
in melting metals, in decocting, preparing, extracting and distilling
herbs, roots; I like it also for the sake of the allegory and secret
signification, which is exceedingly fine, touching the resurrection of the 
dead at the last day."

- Martin Luther's Table talk

Gustavus Adolphus also has alchemical ties, having supposedly
witnessed an alchemical demonstation in 1620.

Around Mayday 2001, you recieved a gift of silver and a larger gift of
gold. Perhaps a metaphor for the transmutation of silver to gold?

One item that is constantly referred to is the Brasher Doubloon, also
gold.

Anyway, I could go on about this, but you see the point, I hope. It
seems to me that Alchemy is the only field that would tie together such
diverse fields as linguistics, religion, physics, Kaballah, numerology,
and everything else that's been thrown out.

Perhaps we're dealing with a group of people who've created (or are in
the process of creating) a modern Philosopher's Stone. There would be
ample reason to keep such a thing secret and well-protected.

I'm afraid this e-mail has been rather unfocused and random. If you
think it will be helpful, I will continue to research and catalog 
possible alchemical/magical references.

Yours,
Bitter The Clown