Dear David & Fellow Twainians who have an interest in this topic~

Albert Bigelow Paine's 1912 biography contains what you are looking for, it
was written in 1910.  Under the chapter "The Voyage home" (page 1566, volume
3 of the 3 volume edition), Paine describes it as "the last bit of continued
writing he ever did", and referred to it as "Advice."  Actually it isn't
Mark Twain's last handwritten manuscript, as that is in reality a humorous
writing he wrote to angelfish Helen Allen just before departing Bermuda in
April 1910 (in my private collection, soon to be written about in my
forthcoming website www.MarkTwainCollector.com).

You may find it of interest that Mark Twain wrote about his doubts regarding
the afterlife in a poem to Mrs. Thomas K. Beecher (the wife of the very
minister who presided over the Sam & Livy Clemens wedding ceremony).  As
Paine's 1912 biography on page 1001 volume 2 explains, Mrs. Beecher
presented Twain with three flat stones to write an agreement between them.
Mrs. Beecher's position was there was an afterlife, Twain's that there
wasn't any.  It is so short I'll just go ahead and type it up here from the
original draft copy in my private collection to correct a few errors in
Paine's transcription:

"If you prove right and I prove wrong
   A million years from now,
In language plain and frank and strong
   My error I'll avow
To your dear mocking face.

If I prove right, by God His grace
  Full sorry I shall be,
For in that solitude no trace
  There'll be of you and me
      Nor of our vanished race.

A million years, O patient stone,
  Youv'e waited for this message:
Deliver it, a million hence.
  [survivor pays expressage.]

                         M. T.   July 2, 1895

NOTE: the original stones are in the collection of Elmira College, presented
to them in 1962.  See Mark Twain in Elmira by Jerome & Wisbey for an
illustration and more information.  -- I understand this book  is currently
being updated and is going to be reissued by Elmira College in the near
future.

 Of course, Mark Twain also believed in the possibility of an afterlife ,
and actually helped people in their own attempts to contact loved ones from
beyond the grave.  Twain himself encountered several first hand experiences
of mental telepathy and death, and even an experience of  his daughter
Jean's communication with him after her death.  Therefore, before Twain came
to have his turn, it is evident he gave the afterlife at least a 50% chance
of being true.

Twainiacally Yours,

Bob