I took the list of good words and examined the contexts of all "gallows" letters:
  
    cat bio-j-jsa.wds \
      | jsa2hoc \
      | enum-contexts -vCTX=1 -vPAT='[HP]' \
      | wfreq4
      
        710 AHc
        361 AHa
        320 cHc
        319 oHc
        170 oHa
        146 eHc
        108  Hc
         90 AH9
         80 ?Hc
         72 cH9
         57 9Hc
    
  Statistics of \c/ strings:

    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vCTX=0 -vPAT='cc*' \
      | wfreq4
      
        860 c
       1317 cc
        884 ccc
        145 cccc
          1 ccccc
          
  These numbers suggest that \cc/ may be a single letter.
  
  Let's look at the frequencies of single \c/:
   
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vCTX=00 -vPAT='[^c]c[^c]' \
      | wfreq4

        399 Hc8             9 qcH             4 zce             1 rca
        247 Hc9             8 zca             2 acH             1 qc9
         30 zc8             8 zcH             2 Pca             1 Pco
         25 zco             7 Hcz             2 Pc9             1 Pc8
         23 Hco             6 Hca             2 8c8             1 9cP
         13 zc9             6 AcH             1 zcz             1 9cH
         10 ocH

  It seems that single \c/s are all associated with \z/,
  \H/, or \P/.  I will try to remove the cHc and cPc sequences and see 
  what happens:
  
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | sed -e 's/c[HP]c/X/g' \
      | enum-contexts -vCTX=00 -vPAT='[^c]c[^c]' \
      | wfreq4

        380 Hc8            25 zco             4 zce             1 qc9
         78 Hc9            19 Hco             2 qcH             1 Xcz
         60 zcX            13 zc9             2 Hca             1 Xco
         30 zc8             8 zca             2 8c8             1 AcX
         30 Xc9             7 Hcz             1 zcz             1 9cP
         29 Xc8             5 zcH             1 rca
    
  It seems that \c8/ and \c9/ are also major sources of single \c/s
      
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | sed \
          -e 's/c[HP]c/X/g' \
          -e 's/zc/Z/g' \
          -e 's/c8/K/g' \
          -e 's/c9/W/g' \
      | enum-contexts -vCTX=00 -vPAT='[^c]c[^c]' \
      | wfreq4
      
        315 HcK             9 Zca             2 rcW             1 Zcz
        166 HcW             6 XcK             2 qcH             1 ZcP
         52 ZcK             6 AcK             2 XcW             1 Xcz
         48 ZcX             5 PcK             2 Hcz             1 Xco
         40 Zco             5 HcZ             2 Hca             1 PcW
         34 ZcW             5 8cK             1 rca             1 AcX
         25 ZcH             3 qcK             1 qcW             1 AcW
         19 Hco             3 KcW             1 ocW             1 9cP
         15 ecK             3 8cW             1 ocK             1 9cK
         14 ecW
     
  Not very illuminating. Let's examine again the \c/ strings in context: 

    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vCTX=1 -vPAT='cc*' \
      | wfreq4

     401 Hc8            11 8ccc8           3 Hcccc9          1 ocP
     347 Hcc8           11  ccca           3 8cco            1 eccz
     322 zcc8           10  cccz           3 8ccco           1 eccccz
     255 Hc9            10  cP             3 8c8             1 ecccco
     200 Hcc9            9 zcca            3  ccccz          1 ecccP
     192  ccc8           9 qcH             3  ccP            1 ecca
     116 zcc9            9 Pcc8            2 zcccP           1 eccP
      97 eccc8           9  cce            2 zc              1 eccH
      90  cccH           8 zca             2 rcccH           1 ecc
      82 zccH            8 zcH             2 rcc9            1 Pco
      67  ccc9           8 Pcc9            2 occc8           1 Pcca
      59 zcccH           7 Hcz             2 ecce            1 Pc8
      53 Pccc8           7 8cc9            2 eccca           1 HccccH
      52 zccc8           7  cccP           2 acH             1 Hc
      51  ccccH          6 rccc9           2 Pcccc9          1 Accc9
      42 eccc9           6 rccc8           2 Pca             1 AccH
      40 zcco            6 eccccH          2 Pc9             1 Acc9
      37 Hccc8           6 Hca             2 Hccco           1 9ccco
      34 zccc9           6 Acc8            2 Hcccc8          1 9ccccz
      31 zc8             6 AcH             2 Accc8           1 9cccc9
      31  cccc9          6 9ccc8           2 9ccccH          1 9cccc8
      26 zco             6  cc9            1 zcz             1 9ccc9
      25 Hco             5 eccco           1 zccz            1 9cc8
      25  ccco           5 ecccc8          1 zccccH          1 9cP
      24 Hccc9           5 8cc8            1 zcccc9          1 9cH
      22  cc8            4 zce             1 rccz            1 8cccco
      20  cccc8          4 zcccz           1 rcccz           1 8cccc9
      17  cco            4 zccP            1 rcccc9          1 8cccc8
      17  cH             4 ecccc9          1 rcccc8          1 8cccH
      15 ecc8            4 Pccco           1 rccca           1 8ccc9
      14 zc9             4 Hccz            1 rca             1 8c9
      14 ecc9            4 Hcca            1 qccc8           1  cccco
      14  ccH            3 zccco           1 qcc9            1  ccccco
      13  cca            3 qcc8            1 qc9             1  cccca
      11 ocH             3 ecco            1 occca           1  ccccP
      11 Pccc9           3 ecccH           1 occ9            1  ca
      11 Hcco            3 Pcco            1 occ8

  Let's look more closely at the \Hc^*8/ strings:

    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vCTX=1 -vPAT='Hcc*8' \
      | wfreq4
      
     198 AHc89          14  Hccc89         2 AHcccc89        1 cHc8
     184 AHcc89         14  Hcc89          2 9Hcc8a          1 AHccc8
      85 oHc89          11 AHccc89         2 8Hc89           1 AHcc8a
      59 oHcc89          9 oHc8a           2  Hcc8           1 AHc8z
      31 cHcc89          6 oHccc89         1 oHcc8a          1 AHc8o
      29 eHc89           5 AHcc8           1 oHc8c           1 AHc8c
      27 eHcc89          5 AHc8a           1 oHc8            1  Hccc8a
      26  Hc89           3 oHcc8           1 eHcc8           1  Hcc8o
      20 cHc89           3 AHc8            1 eHc8c           1  Hcc8a
      15 9Hc89           2 eHccc89         1 eHc8            1  Hc8a
      14 9Hcc89          2 cHccc8          1 cHcc8c

  Curiously, so the string \Hc*8/ is almost always followed by \9/.
  I wonder if that is true in general:
  
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vLCTX=0 -vRCTX=2 -vPAT='c8' \
      | wfreq4

    1526 c89             5 c8oe            2 c8av            1 c89z
      45 c8              4 c8cc            1 c8zc            1 c89o
      24 c8ar            4 c8af            1 c8c9            1 c89H
      22 c8ae            3 c8or            1 c8c8            1 c89A
      10 c8am            3 c89e            1 c8an

  It does seem that \c8/ is almost always followed by \9/, and occasionally
  by end-of-word. Let's look at the left context:
  
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vLCTX=1 -vRCTX=0 -vPAT='cc*8' \
      | wfreq4
  
     401 Hc8            31 zc8             6 9ccc8           1 rcccc8
     347 Hcc8           22  cc8            5 ecccc8          1 qccc8
     322 zcc8           20  cccc8          5 8cc8            1 occ8
     192  ccc8          15 ecc8            3 qcc8            1 Pc8
      97 eccc8          11 8ccc8           2 occc8           1 9cccc8
      53 Pccc8           9 Pcc8            2 Hcccc8          1 9cc8
      52 zccc8           6 rccc8           2 Accc8           1 8cccc8
      37 Hccc8           6 Acc8            2 8c8             1  c8

  Let's look at fout \c/s:
  
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vLCTX=0 -vRCTX=1 -vPAT='cccc' \
      | wfreq4
  
      61 ccccH          30 cccc8           3 cccco           1 cccca
      44 cccc9           5 ccccz           1 ccccc           1 ccccP

    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vLCTX=1 -vRCTX=0 -vPAT='cccc' \
      | wfreq4
  
     109  cccc           6 Hcccc           3 8cccc           2 rcccc
      17 ecccc           5 9cccc           2 zcccc           2 Pcccc
      
    Let's examine the contexts of \zc/:
    
    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vLCTX=1 -vRCTX=0 -vPAT='zc' \
      | wfreq4

     580  zc            31 8zc            13 rzc             5 czc
     108 ezc            19 9zc             9 zzc             4 ozc
      41 Hzc            14 Pzc

    cat bio-j-jsa-gut.wds \
      | jsa2hoc \
      | enum-contexts -vLCTX=0 -vRCTX=1 -vPAT='zc' \
      | wfreq4

     730 zcc            14 zc9             8 zcH             2 zc
      31 zc8             8 zca             4 zce             1 zcz
      26 zco


  It is time to change my ad-hoc encoding to reflect the consonant/vowel
  theory (as suggested by Grove).
  
  We have identified several categories of symbols:
  
    \iiiu/, \iiu/, \iis/, \ij/  
    
        The ziggies: strictly final, preceded always by \ci/ or,
        more rarely, by \o/.
        
    \cy/ 
    
        Almost always final, but occasionaly followed by other letters.
        Preceded by about the same letters as \ci/; indeed, it is 
        probably the final form of \ci/.
        
    \cg/ 
    
        May be followed by many letters, most often \cy/ and \ci/.
        Almost always prededed by \c/, or initial; rarely by \ix/
        or \o/.
        
    \cs/ 
    
        Most often followed by \c/, somewhat less often by \o/,
        \ci/, or word break.  Most often initial, but also 
        preceded by \ix/, gallows, \c/, \cy/, \cg/, \is/.
        
    \lg/, \qg/, \lj/, \qj/ 
    
        The capitals: Very similar to each other, different from the rest.
        probably to be combined with \c/ on both sides.
        
    \qo/ 
    
        Strictly initial, almost always followed by a capital.
    
    \ix/ 
     
        Usually initial or preceded by \ci/ or \o/;
        followed by any letter except ziggies and \qo/,
        \ix/, \is/
        
    \is/ 
    
        Similar to \ix/ except that it cannot be
        followed by capitals or \cg/, either.

    \ci/
    
        May be followed only by the ziggies, \ix/, or \ir/
        only.  Often follows a capital, but also \cg/,
        \cs/, \c/, \ix/, \is/, or word break.
        
    \o/ 
    
        Similar to \a/, but is very often word-initial.
                   
  With these considerations, I defined a new encoding,
  "hic": 
  
      jsa2hic
      -------------------------------------------------
      #! /n/gnu/bin/sed -f
      # Recoding superanalytic to ad-hoc encoding:
      s/ij/J/g
      s/ix/I/g
      s/ci/S/g
      s/iiiu/M/g
      s/iiu/N/g
      s/iis/L/g
      s/is/C/g
      s/csc/Z/g
      s/cg/U/g
      s/cy/S/g
      s/qo/W/g
      s/qj/A/g
      s/qg/E/g
      s/lj/Y/g
      s/lg/O/g
      s/o/R/g
      s/cc/T/g
     -------------------------------------------------

    extract-words-from-interlin \
        -recode jsa2hic \
        -chars "AEIOUYWSRTMNLc" \
        bio-j-jsa.evt \
        bio-j-hic

     lines   words     bytes file        
    ------ ------- --------- ------------
      7054    7054     41600 bio-j-hic.wds
      1934    1934     15117 bio-j-hic.dic
      4626    4626     26296 bio-j-hic-gut.wds
       800     800      5150 bio-j-hic-gut.dic
       875     875      2655 bio-j-hic-fun.wds
        33      33       189 bio-j-hic-fun.dic
      1553    1553     12649 bio-j-hic-bad.wds
      1101    1101      9778 bio-j-hic-bad.dic

                  S     T     R     L     N     Z     H     Q     A     E     O     U     c   TOT
        ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
            .   161   965   282    78   215   727   362  1215     .     .     .     .   621  4626
      S  2781     1     3   410   274    69    24    11     2    33    19   108   328    18  4081
      T    14     1     .   758   170   502     6    11     4     4     1     1     9    17  1498
      Q     7     4     1   134     7  1044     .     7     1     .     .     1     .    17  1223
                                                             
      R   824   113   105     3     2   190   115    53     1     .     .     .     .   205  1611
      L   396    64    36     .     .     .    13     2     .     .     .     .     .    21   532
      N    12   807   110     6     .     .    55     6     .     .     .     .     .  1420  2416
      Z    41    72    63     1     .     3     9     3     .     .     .     .     .   823  1015
      H    49  1939    37     3     1     4    31     1     .     .     .     .     .    37  2102
                                                             
      A    36     .     1     .     .     .     .     .     .     .     .     .     .     .    37
      E    19     1     .     .     .     .     .     .     .     .     .     .     .     .    20
      O   109     .     1     .     .     .     .     .     .     .     .     .     .     .   110
      U   334     3     .     .     .     .     .     .     .     .     .     .     .     .   337
      c     4   915   176    14     .   389    35  1646     .     .     .     .     .  3509  6688
        ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
    TOT  4626  4081  1498  1611   532  2416  1015  2102  1223    37    20   110   337  6688 26296

    Next-symbol probability (× 99):

                  N     R     L     S     T     Z     Q     H     A     E     O     U     c   TOT
        ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
            .     5     6     2     3    21    16    26     8     .     .     .     .    13    99
      N     .     .     .     .    33     5     2     .     .     .     .     .     .    58    99
      R    51    12     .     .     7     6     7     .     3     .     .     .     .    13    99
      L    74     .     .     .    12     7     2     .     .     .     .     .     .     4    99
      S    67     2    10     7     .     .     1     .     .     1     .     3     8     .    99
      T     1    33    50    11     .     .     .     .     1     .     .     .     1     1    99
      Z     4     .     .     .     7     6     1     .     .     .     .     .     .    80    99
      Q     1    85    11     1     .     .     .     .     1     .     .     .     .     1    99
      H     2     .     .     .    91     2     1     .     .     .     .     .     .     2    99
      A    96     .     .     .     .     3     .     .     .     .     .     .     .     .    99
      E    94     .     .     .     5     .     .     .     .     .     .     .     .     .    99
      O    98     .     .     .     .     1     .     .     .     .     .     .     .     .    99
      U    98     .     .     .     1     .     .     .     .     .     .     .     .     .    99
      c     .     6     .     .    14     3     1     .    24     .     .     .     .    52    99
        ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
    TOT    17     9     6     2    15     6     4     5     8     0     0     0     1    25 26296

    Previous-symbol probability (× 99):

                  N     R     L     S     T     Z     Q     H     A     E     O     U     c   TOT
        ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
            .     9    17    15     4    64    71    98    17     .     .     .     .     9    17
      N     .     .     .     .    20     7     5     .     .     .     .     .     .    21     9
      R    18     8     .     .     3     7    11     .     2     .     .     .     .     3     6
      L     8     .     .     .     2     2     1     .     .     .     .     .     .     .     2
      S    60     3    25    51     .     .     2     .     1    88    94    97    96     .    15
      T     .    21    47    32     .     .     1     .     1    11     5     1     3     .     6
      Z     1     .     .     .     2     4     1     .     .     .     .     .     .    12     4
      Q     .    43     8     1     .     .     .     .     .     .     .     1     .     .     5
      H     1     .     .     .    47     2     3     .     .     .     .     .     .     1     8
      A     1     .     .     .     .     .     .     .     .     .     .     .     .     .     0
      E     .     .     .     .     .     .     .     .     .     .     .     .     .     .     0
      O     2     .     .     .     .     .     .     .     .     .     .     .     .     .     0
      U     7     .     .     .     .     .     .     .     .     .     .     .     .     .     1
      c     .    16     1     .    22    12     3     .    78     .     .     .     .    52    25
        ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
    TOT    99    99    99    99    99    99    99    99    99    99    99    99    99    99 26296


    cat bio-j-jsa.wds \
      | /n/gnu/bin/awk -f foo.awk \
      | sort | uniq -c | sort -nr | expand \
      > bio-j-jsa-wpairs.freq