As gratifying as it has been to see the read count on this thread growing after my update earlier this month (which will probably lead to the release of the first several chapters of _The (Duh!) Voynich Code_ next April Fools' Day), ideally I'd like to be remembered for more substantial contributions. As a result, I thought I would take advantage of the recent visibility of this thread to point people to the open-source Awk language "Swiss Army knife" text analysis tool I posted in You are not allowed to view links. 
Register or 
Login to view.. If the low download count represents lack of access to an awk interpreter or issues with the documentation in the comments and the file containing examples of the tool's output, I'm happy to work on adding info on getting awk working under Windows or clarifying the command line options. While this is going to get mangled (at least in part because of  the lack of a fixed-width font option), here's a taste of the info it can generate from the input text sample (note that while the examples use Currier from the D'Imperio transcription, you can use the transcription scheme and text of your choice or analyze natural language texts for comparison):
Example 2: Comparing 20 most-frequent contexts of word-initial '9' (two 
glyphs before the space and one glyph after the '9') between Herbal A and
Biological B.
bash-3.1$ cat HerbA.txt | sed 's/^...... //g' | awk -f ekg2Awk.txt k=5 hz=1 TE=20 SC='-#/' RE='../9.'
#  33702 char 'VAS92/9FAE...E/SOE/8AM#'
# Input alphabet (40 'letters'): 'VAS92/FERPMZOQ8-XN*DUC$TWY#I3HJB0,4K67LG'
# Vowels found by Sukhotin's method excluding digrams containing characters
# in '-#/': O A 9 C 0 6 
#  RE = '../9.'
# XRE = '^$'
# MinCt = 0 (12417 types, 33698 tokens)
#  k  NTyp  NTok  Hk (bits)  PctFreq1  Typ/Tok  k-grams
#  5  12417  33698  12.409070  0.636225 0.36848  all
#  5    121    285  6.179331  65.289256 0.42456  in RE & not in XRE & ct >= MinCt
# Max possible H5: all tokens = 13.600029 bits, RE tokens =  6.918863 bits
# Selected = 0.9745 pct of types, 0.8457 pct of tokens
  kgram:  OR/9P  OR/9F  OE/9F  AM/9F  AM/9P  OE/9P  S9/9P  OR/9/  C9/9P  C9/9F
  Rank:      1      2      3      4      5      6      7      8      9    10
  Count:    22    15    14    12    11    10      9      8      8      6
AllFreq: 0.0007 0.0004 0.0004 0.0004 0.0003 0.0003 0.0003 0.0002 0.0002 0.0002
REFreq: 0.0772 0.0526 0.0491 0.0421 0.0386 0.0351 0.0316 0.0281 0.0281 0.0211
RECmFrq: 1.0000 0.9228 0.8702 0.8211 0.7789 0.7404 0.7053 0.6737 0.6456 0.6175
  kgram:  AR/9F  89/9P  S9/9F  S9/98  C2/9F  AR/9P  AN/9F  ZO/9P  ZO/9F  Q9/9P
  Rank:    11    12    13    14    15    16    17    18    19    20
  Count:      6      6      5      4      4      4      4      3      3      3
AllFreq: 0.0002 0.0002 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001
REFreq: 0.0211 0.0211 0.0175 0.0140 0.0140 0.0140 0.0140 0.0105 0.0105 0.0105
RECmFrq: 0.5965 0.5754 0.5544 0.5368 0.5228 0.5088 0.4947 0.4807 0.4702 0.4596
bash-3.1$ cat BioB.txt | sed 's/^...... //g' | awk -f ekg2Awk.txt k=5 hz=1 TE=20 SC='-#/' RE='../9.'
#  35485 char 'VSC89FAR9/...OPOE/SC89-'
# Input alphabet (34 'letters'): 'VSC89FAR/O4Z-NE2JMPXBQD*TULYW36G5H'
# Vowels found by Sukhotin's method excluding digrams containing characters
# in '-#/': C O A 9 V L Y 
#  RE = '../9.'
# XRE = '^$'
# MinCt = 0 ( 7966 types, 35481 tokens)
#  k  NTyp  NTok  Hk (bits)  PctFreq1  Typ/Tok  k-grams
#  5  7966  35481  10.703298  0.464474 0.22451  all
#  5    50    79  5.268988  74.000000 0.63291  in RE & not in XRE & ct >= MinCt
# Max possible H5: all tokens = 12.959640 bits, RE tokens =  5.643856 bits
# Selected = 0.6277 pct of types, 0.2227 pct of tokens
  kgram:  89/9F  89/9P  C9/9P  C9/9F  AR/9P  AN/9P  P9/9F  C8/9F  AR/9F  AN/9F
  Rank:      1      2      3      4      5      6      7      8      9    10
  Count:    10      6      3      3      3      3      2      2      2      2
AllFreq: 0.0003 0.0002 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001
REFreq: 0.1266 0.0759 0.0380 0.0380 0.0380 0.0380 0.0253 0.0253 0.0253 0.0253
RECmFrq: 1.0000 0.8734 0.7975 0.7595 0.7215 0.6835 0.6456 0.6203 0.5949 0.5696
  kgram:  AN/98  AM/98  AE/9Z  S9/9F  S2/98  Q9/9P  Q9/9O  Q9/9F  OR/9Z  OR/9P
  Rank:    11    12    13    14    15    16    17    18    19    20
  Count:      2      2      2      1      1      1      1      1      1      1
AllFreq: 0.0001 0.0001 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
REFreq: 0.0253 0.0253 0.0253 0.0127 0.0127 0.0127 0.0127 0.0127 0.0127 0.0127
RECmFrq: 0.5443 0.5190 0.4937 0.4684 0.4557 0.4430 0.4304 0.4177 0.4051 0.3924
bash-3.1$ 
Example 3: Print the 20 most-frequent Herbal A word types that 
a) match Zattera's slot model for "regular" (not "separable") words [1], but
b) do not match Tiltman's prefix/suffix model [2]
[1]: strictly speaking, the '[8DERJNGTKMHUL3105]' part of the regex should 
    be modified to something like '((I?I?I?8)|[DERJNGTKMHUL3105])', but in 
    practice it doesn't matter...
[2]: assuming both prefix and suffix have to be non-empty
bash-3.1$ cat HerbA.txt | sed 's/^...... //g' | sed 's.[/#-]. .g' | awk -f ekg2Awk.txt hz=2 WL=1 XRE='^((4?O[FVBP])|[SZ82])((A[DNM3RTU0EGH1])|(O[ER])|(CC?C?8?9))$' RE='^[428]?[O9]?[ER]?[PFBV]?[SZ]?[QXWY]?(CC?C?)?[28]?[OA]?[8DERJNGTKMHUL3105]?9?$'
# Input alphabet (37 'letters'): 'VAS92FERPMZOQ8XN*DUC$TWYI3HJB0,4K67LG'
#  RE = '^[428]?[O9]?[ER]?[PFBV]?[SZ]?[QXWY]?(CC?C?)?[28]?[OA]?[8DERJNGTKMHUL3105]?9?$'
# XRE = '^((4?O[FVBP])|[SZ82])((A[DNM3RTU0EGH1])|(O[ER])|(CC?C?8?9))$'
# MinCt = 0 ( 2224 types,  7121 tokens)
# 
# Word frequency and length histograms: all words
# 
# TypeCount  2224  TokenCount  7121  AvgTypeLen  4.72  AvgTokLen  3.73
# Number of words with given number of occurances:
# NOcc :    1    2    3    4    5    6    7    8    9  10  11  12  13 (>=14)
# NWord: 1562  253  114  58  42  26  22  10  16  10  10  12    8  81 
# 
# Length:    1    2    3    4    5    6    7    8    9  10  11  12  13  14
# % Type:  0.7  3.9 14.4 25.0 29.0 17.1  7.4  1.9  0.4  0.1  0.0  0.0  0.0  0.0 
# % Tok :  3.3 12.0 35.0 22.3 16.9  7.3  2.5  0.6  0.1  0.0  0.0  0.0  0.0  0.0 
# Type length: mean    4.717 mode  5; token length: mean    3.732 mode  3
# 
# Word frequency and length histograms: selected words
# 
# TypeCount  1055  TokenCount  3817  AvgTypeLen  4.16  AvgTokLen  3.44
# Number of words with given number of occurances:
# NOcc :    1    2    3    4    5    6    7    8    9  10  11  12  13 (>=14)
# NWord:  610  162  78  43  28  18  18    6  15    9    7    7    6  48 
# 
# Length:    1    2    3    4    5    6    7    8    9  10  11  12  13  14
# % Type:  1.2  6.8 20.5 32.8 26.1 10.2  2.0  0.4  0.0  0.0  0.0  0.0  0.0  0.0 
# % Tok :  5.7 21.8 23.7 27.5 15.7  5.0  0.7  0.1  0.0  0.0  0.0  0.0  0.0  0.0 
# Type length: mean    4.162 mode  4; token length: mean    3.438 mode  4
#
# Zipf's Law fit to  25 most-frequent selected words:
#    ln(freq) = -0.569149 * ln(rank) + 5.050078
#    Average residual -0.0000000 (SD 0.1139755), RMSE = 0.1139755
# 
#  NTyp  NTok  H  (bits)  PctFreq1  Typ/Tok  Words
#  2224  7121  9.350571  70.233813 0.31232  all
#  1055  3817  8.693055  57.819905 0.27640  in RE & not in XRE & ct >= MinCt
# Selected = 47.4371 pct of types, 53.6020 pct of tokens
  kgram:    89    S9      2    Q9    ZO    Z9    OE  4OPS9    OR    QOE
  Rank:      1      2      3      4      5      6      7      8      9    10
  Count:    113    102    94    88    83    52    49    47    45    44
AllFreq: 0.0159 0.0143 0.0132 0.0124 0.0117 0.0073 0.0069 0.0066 0.0063 0.0062
REFreq: 0.0296 0.0267 0.0246 0.0231 0.0217 0.0136 0.0128 0.0123 0.0118 0.0115
RECmFrq: 1.0000 0.9704 0.9437 0.9190 0.8960 0.8742 0.8606 0.8478 0.8355 0.8237
  kgram:    QOR    OP9      9    SO  4OFS9    OF9  OPS9  SCOR    8AJ  SO89
  Rank:    11    12    13    14    15    16    17    18    19    20
  Count:    43    41    40    37    34    31    30    29    29    28
AllFreq: 0.0060 0.0058 0.0056 0.0052 0.0048 0.0044 0.0042 0.0041 0.0041 0.0039
REFreq: 0.0113 0.0107 0.0105 0.0097 0.0089 0.0081 0.0079 0.0076 0.0076 0.0073
RECmFrq: 0.8122 0.8009 0.7901 0.7797 0.7700 0.7611 0.7529 0.7451 0.7375 0.7299
bash-3.1$