Some letters aren't letters

[Torsten]

Without enumerating them all, the main one (in my opinion) is the pairing of characters. There are several pairs that can be substituted for each other almost arbitrarily:

ch / Sh
k / t
f / p
l / r
o / qo  (at word start)

However, the frequencies of the resulting words are not evenly distributed, so it does not look like something arbitrary.

It seems to me that by saying that you expect evenly distributed frequencies you presuppose a homogeneous text and that it doesn't depend on the context if it is possible to replace for instance [l] with [r] or [k] with [t]. The text is not homogenous and it depends on the context if a glyph can be substituted. Therefore it is indeed not possible to say that [k] is always a substitute for [t]. But this observation doesn't exclude statements like [kch] is a possible substitute for [tch].

1) The text is not homogenous. If we compare the word frequencies for the first three Quires 1, 2 and 3 (all in Herbal and Currier A) we can see nonuniform distributions. For instance the word [sho] is 7th most frequent word in Quire 1 and the 9th most frequent word in Quire 3 but only the 37th frequent word in Quire 2.

The 20 most frequent word types in Quire 1:
daiin (56), chol  (50), chor   (47), shol  (31), cthy  (24), 
s     (23), sho   (21), dain   (18), chy   (16), dar   (14),
dy    (14), shor  (14), cthol  (14), dol   (13), or    (12),
y     (11), shey  (11), chaiin (11), chey  (10), dal   ( 9)

The 20 most frequent word types in Quire 2:
daiin (61), dy    (34), chol   (28), cthy  (27), chor  (20),
chy   (16), shor  (14), s      (13), dain  (13), cthor (12),
y     (11), qotchy (9), shol   ( 9), kchy  ( 9), otchy ( 9),
dor   ( 8), qoty   (8), dchy   ( 8), shy   ( 8), chody ( 7)

The 20 most frequent word types in Quire 3:
daiin  (70), chol  (37), chor  (30), dar     (22), s     (21),
cthy   (17), ol    (17), or    (17), sho     (16), dy    (15),
shy    (15), y     (14), shol  (14), qokchy  (14), dal   (12),
qotchy (12), chy   (11), otchy (10), dor     ( 9), cthor ( 9)

2) It depends on the context if a glyph is replaceable. If we order the words by their similarity we can see that the frequencies for only some similar words are related. For instance in all three quires the words ending in [-ol] and  [-or] are more frequent then words ending in [-al] and [-ar] with [dal] and [dar] as exception. Also the frequencies for the words with a group [tch] match with the frequencies for there [kch] counterparts even if such groups are more common in Quire 3 and 2 then in Quire 1. On the other side this is not true for words with [cth] or [ckh] since words with [ckh] are rare. If you now compare the statistics for [l]/[r] and [t]/[k] for the whole manuscript they include also the statistics for the words that doesn't match your expectations like [dal], [dar] and words with [cth] vs. words with [ckh].

The 20 most frequent word types in Quire 1 as grid including similar word types:
aiin ( 3) daiin (56) chaiin (11) shaiin ( 4) cthaiin ( 4) ckhaiin ( 1)
ain  (--) dain  (18) chain  (--) shain  ( 1) cthain  (--) ckhain  (--)
ar   ( 3) dar   (14) char   ( 8) shar   ( 3) cthar   ( 7) ckhar   ( 1)
al   ( 3) dal   ( 9) chal   ( 4) shal   (--) cthal   ( 2) cthal   ( 1)
ol   ( 9) dol   (13) chol   (50) shol   (31) cthol   (14) ckhol   (--)
or   (12) dor   ( 7) chor   (47) shor   (14) cthor   ( 6) ckor    (--)
y    (11) dy    (14) chy    (16) shy    ( 6) cthy    (24) ckhy    ( 8)
o    ( 3) do    ( 7) cho    ( 7) sho    (21) ctho    ( 1) ckho    ( 1)
ey   (--) dey   ( 1) chey   (10) shey   (11)
eey  ( 1) deey  (--) cheey  ( 3) sheey  ( 7)

tchol (--) otchol ( 5) qotchol ( 1) qokchol (--) okchol ( 1) kchol ( 1)
tchor ( 4) otchor ( 5) qotchor (--) qokchor ( 1) okchor ( 2) kchor ( 3)
tchy  ( 2) otchy  ( 4) qotchy  ( 3) qokchy  ( 3) okchy  ( 1) kchy  ( 4)
tcho  (--) otcho  ( 1) qotcho  ( 3) qokcho  ( 1) okcho  (--) kcho  ( 1)

The same word grid for Quire 2:
aiin ( 5) daiin (61) chaiin ( 5) shaiin ( 2) cthaiin ( 2) ckhaiin ( 1)
ain  (--) dain  (13) chain  (--) shain  (--) cthain  (--) ckhain  (--)
ar   ( 1) dar   ( 5) char   ( 1) shar   ( 1) cthar   ( 1) ckhar   (--)
al   (--) dal   ( 3) chal   (--) shal   (--) cthal   (--) ckhal   (--)
ol   ( 2) dol   ( 3) chol   (28) shol   ( 9) cthol   ( 2) ckhol   (--)
or   ( 5) dor   ( 8) chor   (20) shor   (14) cthor   (12) ckhor   (--)
y    (11) dy    (34) chy    (16) shy    ( 8) cthy    (27) ckhy    ( 3)
o    ( 1) do    (--) cho    ( 1) sho    ( 5) ctho    ( 2) ckho    (--)
ey   (--) dey   (--) chey   ( 4) shey   ( 6)
eey  (--) deey  (--) cheey  (--) sheey  (--)

tchol ( 2) otchol ( 3) qotchol ( 2) qokchol ( 2) okchol ( 1) kchol ( 4)
tchor ( 2) otchor ( 5) qotchor ( 5) qokchor ( 3) okchor ( 4) kchor ( 2)
tchy  ( 3) otchy  ( 9) qotchy  ( 9) qokchy  ( 6) okchy  ( 5) kchy  ( 9)
tcho  (--) otcho  ( 2) qotcho  ( 1) qokcho  ( 1) okcho  (--) kcho  (--)

The same word grid for Quire 3:
aiin ( 2) daiin (70) chaiin ( 1) shaiin ( 3) cthaiin ( 2) ckhaiin (--)
ain  (--) dain  ( 6) chain  (--) shain  ( 2) cthain  ( 1) ckhain  (--)
ar   ( 6) dar   (22) char   ( 5) shar   ( 1) cthar   ( 5) ckhar   (--)
al   (--) dal   (12) chal   ( 2) shal   (--) cthal   ( 3) ckhal   (--)
ol   (17) dol   ( 7) chol   (37) shol   (14) cthol   ( 9) ckhol   ( 1)
or   (17) dor   ( 9) chor   (30) shor   ( 6) cthor   ( 9) ckhor   ( 1)
y    (14) dy    (15) chy    (11) shy    (15) cthy    (17) ckhy    ( 3)
o    ( 3) do    ( 1) cho    ( 6) sho    (16) ctho    ( 2) ckho    (--)
ey   (--) dey   (--) chey   ( 8) shey   ( 2)
eey  (--) deey  ( 1) cheey  ( 4) sheey  ( 2)

tchol ( 3) otchol ( 5) qotchol ( 4) qokchol ( 8) okchol ( 1) kchol ( 5)
tchor ( 2) otchor ( 1) qotchor ( 1) qokchor ( 2) okchor ( 3) kchor ( 4)
tchy  ( 5) otchy  (10) qotchy  (12) qokchy  (14) okchy  ( 4) kchy  ( 4)
tcho  ( 1) otcho  (--) qotcho  (--) qokcho  (--) okcho  ( 1) kcho  (--)