I have scanned in a very long document.  My scanner requires me to
scan first the odd pages (1-99) then then even pages (2-100).  I now
have two PDF documents.  Is there any way within Acrobat or with a
third party tool to merge automatically the two documents into one? 
I want page 1, 2, 3, 4, etc. in the correct order.  1 and 3 are now
the first two pages of Document A; 2 and 4 are now the first two pages
of Document B.  This process would be identicall to perfectly
shuffling two separate decks of cards.  At the moment, the only way I
can figure out how to do it is to manually drag the pages of one file
into the other file--a very time consuming process.  Thanks!

Well here's an idea ... For what it's worth:

Insert a special code at the bottom of each page, say '[PB}' then
export both sets to text files, A & B.

Import each file into separate Winword docs and globally replace [PB]
with a manual Page Break ^m (I think).

Then you Mailmerge the two docs and Voila! after you've transferred it
all back to PDF, you've done the biz.

(I think).

Well it was only an idea.

If you still need this done if you upload the two pdf's in question so
I can download them I can probably do it for you

If this is something you need some software to do regularly then post
a clarification