Jason Gary Horn's new book, _Mark Twain and William James: Crafting a
Free Self_ (Univ. of Missouri Press, 1996) might be a good resource
on Twain's religious views.  I just picked it up today and haven't
read much of it yet, but the intro discusses Twain's and James's
views on religion as a personally developed belief system and I
suspect that there will be more on the topic in later chapters.

Jim Zwick
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http://web.syr.edu/~fjzwick/