I "roughly" got it using the DOI txt I linked above.
I tried again with the pre-mapped text you linked to, and got `e o a p s p` which is an anagram for `appose`... perhaps that is the word? "Appose" means "to place (something) in proximity to or juxtaposition with something else." Maybe I'm grasping at straws here...
Offset of +1 yields `b s a i t h` which is an anagram for habits.
Offset of -1 yields `a t a l b t` which is an anagram for Alt-Tab (which is roughly what I'm doing right now to get out of this :p)
I also tried all offsets within 0-7 for each character, to see if "CIPHER" could fit in that range. CI_H_R is possible but there is no P or E within +/- 7 offset of 201 or 337.
Here's the python:
txt="""<<Pasted from http://cipherfoundation.org/older-ciphers/beale-papers/beale-papers-transcription/>>"""
import re
codes = txt.split(' ')
codes = filter(None, codes)
code2word = {}
words = []
for code in codes[0:-1]:
try:
index = re.search(re.compile(ur'\((\d+)\)'), code).group(1)
except:
index = index + 1
word = code.replace('(%d)' % int(index), '')
code2word[int(index)] = word
print index, word
for code in [89, 263, 201, 500, 337, 480]:
word = code2word[code]
print word[0],
Good luck