Return to Answer

(Very) Partial Answer / Work In Progress:

Looking at different character counts, we have the following distribution:

      Count | Doubles | Triples
 T:      32         6         1
 I:      32         0         0
 N:      29         3         1
 K:      41         6         0
 L:      48         3         0
 E:      37         3         0
 R:      23         0         0
 S:      91        24         3
 

This leads me to believe that the character 'S' is some sort of flow control character, instead of a numeral. My best guess so far:

Single S - Character separator
Double S - Word separator
Triple S - Line separator  

Update: Hint 4 half-confirmed this, by saying that the S is a character separator.

One character adds a 0 to the previous character's value. We can figure out which is the multiplier by looking for a ciphertext-character that is never at the start of a plaintext-character. The only character that meets that is I.

One other character is an operator, though of what sort I'm not sure. My best guess is that that character is R, because it never appears as a double, and there are no lines that consist entirely of Rs, and because R is never followed by an I, and after fix by OP, never appears at the end of a character. This means R does something to the value of the next character. My best guess is that it makes that character hold a negative value.

Finally, an answer (which I got barely before the last hint, but didn't type fast enough).
The TINKLERS are going to cheese:

The Bean, in Chicago, at 3:46pm

How I got there:

Looking at different character counts, we have the following distribution:

      Count | Doubles | Triples
 T:      32         6         1
 I:      32         0         0
 N:      29         3         1
 K:      41         6         0
 L:      48         3         0
 E:      37         3         0
 R:      23         0         0
 S:      91        24         3
 

This leads me to believe that the character 'S' is some sort of flow control character, instead of a numeral. My best guess so far:

Single S - Character separator
Double S - Word separator
Triple S - Line separator  

Update: Hint 4 half-confirmed this, by saying that the S is a character separator.

One character adds a 0 to the previous character's value. We can figure out which is the multiplier by looking for a ciphertext-character that is never at the start of a plaintext-character. The only character that meets that is I.

One other character is an operator, though of what sort I'm not sure. My best guess is that that character is R, because it never appears as a double, and there are no lines that consist entirely of Rs, and because R is never followed by an I, and after fix by OP, never appears at the end of a character. This means R does something to the value of the next character. My best guess is that it makes that character hold a negative value.

Using these assumptions, I:

Wrote a java program to brute force all permutations of values for TNKLE (knowing they were valued at 1, 2, 3, 5, and 10). I also took the resulting value of each character mod 40, because there were no possible combinations that wouldn't overflow. Then, I just cycled through all combinations until I got to one that generated readable text! (I know totally inelegant, but hey, the CIA should have supercomputers, right ;) )
This resulted in the following values:

 T: 3
 I: Multiply previous by 10
 N: 1
 K: 10
 L: 5
 E: 2
 R: Next value is negative
 S: Character delimiter 

This revealed the message:

comradepranksters,westrikechicago.at1546,weshallcheese...thebean!

Adding spaces and capitalization, this becomes:
"Comrade pranksters, we strike Chicago. At 1546, we shall cheese... The Bean!"

(Very) Partial Answer / Work In Progress:

Looking at different character counts, we have the following distribution:

      Count | Doubles | Triples
 T:      32         6         1
 I:      32         0         0
 N:      29         3         1
 K:      41         6         0
 L:      48         3         0
 E:      37         3         0
 R:      23         0         0
 S:      91        24         3
 

This leads me to believe that the character 'S' is some sort of flow control character, instead of a numeral. My best guess so far:

Single S - Character separator
Double S - Word separator
Triple S - Line separator  

Update: Hint 4 half-confirmed this, by saying that the S is a character separator.

Working with this, we have the message:

RLLIR
LK
TLET
TKL
KKNKK
EE
LIRL
NKL
LLTL
TRE
EKE
TELN
EIRN
LETLTE
L
EIRE
LILEE
KNKNKNL
KTK
NENN
LTEELE
KLKKLKK
REKI
TNL
NK
RLK
EN
LIRE
KRN
LIRLRE
N
EL
LIL
TIEL
KIEIN
NILI
RELIEI
KKNNK
NTI
TTI
RKLIRE
TEI
L
KRNLI
TL
N
EK
ELI
NNN
TTE
L
RLLI
TTNTTTT
RKRLKI
LIRKRT
KEKLK
RTTILI
KK
TET
ENE
E
KILKI
TINLI
KTN
RKLI

From hint 6:

One character adds a 0 to the previous character's value. We can figure out which is the multiplier by looking for a ciphertext-character that is never at the start of a plaintext-character. The only character that meets that is I.

One other character is an operator, though of what sort I'm not sure. Whatever it is, it can appear at the start or end of a character, because T, N, K, L, E and R all do both. My best guess is that that character is R, because it never appears as a double, and there are no lines that consist entirely of Rs, and because R is never followed by an I.

(Very) Partial Answer / Work In Progress:

Looking at different character counts, we have the following distribution:

      Count | Doubles | Triples
 T:      32         6         1
 I:      32         0         0
 N:      29         3         1
 K:      41         6         0
 L:      48         3         0
 E:      37         3         0
 R:      23         0         0
 S:      91        24         3
 

This leads me to believe that the character 'S' is some sort of flow control character, instead of a numeral. My best guess so far:

Single S - Character separator
Double S - Word separator
Triple S - Line separator  

Update: Hint 4 half-confirmed this, by saying that the S is a character separator.

Working with this, we have the message:

RLLIRE
LK
TLET
TKL
KKNKK
EE
LIRL
NKL
LLTL
TRE
EKE
TELN
EIRN
LETLTE
L
EIRE
LILEE
KNKNKNL
KTK
NENN
LTEELE
KLKKLKK
REKI
TNL
NK
RLK
EN
LIRE
KRN
LIRLRE
N
EL
LIL
TIEL
KIEIN
NILI
RELIEI
KKNNK
NTI
TTI
RKLIRE
TEI
L
KRNLI
TL
N
EK
ELI
NNN
TTE
L
RLLI
TTNTTTT
RKRLKI
LIRKRT
KEKLK
RTTILI
KK
TET
ENE
E
KILKI
TINLI
KTN
RKLI

From hint 6:

One character adds a 0 to the previous character's value. We can figure out which is the multiplier by looking for a ciphertext-character that is never at the start of a plaintext-character. The only character that meets that is I.

One other character is an operator, though of what sort I'm not sure. My best guess is that that character is R, because it never appears as a double, and there are no lines that consist entirely of Rs, and because R is never followed by an I, and after fix by OP, never appears at the end of a character. This means R does something to the value of the next character. My best guess is that it makes that character hold a negative value.

Looking at different character counts, we have the following distribution:

      Count | Doubles | Triples
 T:      32         6         1
 I:      32         0         0
 N:      29         3         1
 K:      41         6         0
 L:      48         3         0
 E:      37         3         0
 R:      23         0         0
 S:      91        24         3
 

This leads me to believe that the character 'S' is some sort of flow control character, instead of a numeral. My best guess so far:

Single S - Character separator
Double S - Word separator
Triple S - Line separator  

Working with this assumption, we have the message:

 

RLLIR-LK-TLET-TKL
 KKNKK EE-LIRL-NKL-LLTL TRE-EKE TELN-EIRN-LETLTE-L-EIRE LILEE-KNKNKNL KTK-NENN-LTEELE KLKKLKK REKI TNL-NK-RLK-EN-LIRE KRN-LIRLRE-N
 EL-LIL TIEL KIEIN-NILI-RELIEI KKNNK NTI-TTI-RKLIRE-TEI L KRNLI-TL-N EK-ELI NNN TTE-L RLLI-TTNTTTT-RKRLKI LIRKRT KEKLK-RTTILI-KK-TET
 ENE-E-KILKI-TINLI-KTN-RKLI

This gives us a few hints as to what some characters are:

Assuming the character is determined by adding the value of each character that makes it, we have a few single character "words":

KKNKK
KLKKLKK
REKI
TIEL
KKNNK
L
NNN

Most likely, these single character "words" are either A (adding up to 1), I (adding up to 9), maybe N or W (14 or 23, for coordinates), or numbers (valued 27-36), or punctuation, that would most likely be part of longer words.
The safest guess is that L has a numerical value of 1, which means an L on its own is an A. It also seems possible, though less directly, that NNN is "I", with N having a numerical value of 3. This also means that an N on its own is "C"

Looking at different character counts, we have the following distribution:

      Count | Doubles | Triples
 T:      32         6         1
 I:      32         0         0
 N:      29         3         1
 K:      41         6         0
 L:      48         3         0
 E:      37         3         0
 R:      23         0         0
 S:      91        24         3
 

This leads me to believe that the character 'S' is some sort of flow control character, instead of a numeral. My best guess so far:

Single S - Character separator
Double S - Word separator
Triple S - Line separator  

Update: Hint 4 half-confirmed this, by saying that the S is a character separator.

Working with this, we have the message:

RLLIR 
LK 
TLET 
TKL 
KKNKK 
EE 
LIRL 
NKL 
LLTL 
TRE 
EKE 
TELN 
EIRN 
LETLTE 
L 
EIRE 
LILEE 
KNKNKNL 
KTK 
NENN 
LTEELE 
KLKKLKK 
REKI 
TNL 
NK 
RLK 
EN 
LIRE 
KRN 
LIRLRE 
N 
EL 
LIL 
TIEL 
KIEIN 
NILI 
RELIEI 
KKNNK 
NTI 
TTI 
RKLIRE 
TEI 
L 
KRNLI 
TL 
N 
EK 
ELI 
NNN 
TTE 
L 
RLLI 
TTNTTTT 
RKRLKI 
LIRKRT 
KEKLK 
RTTILI 
KK 
TET 
ENE 
E 
KILKI 
TINLI 
KTN 
RKLI

From hint 6:

One character adds a 0 to the previous character's value. We can figure out which is the multiplier by looking for a ciphertext-character that is never at the start of a plaintext-character. The only character that meets that is I.

One other character is an operator, though of what sort I'm not sure. Whatever it is, it can appear at the start or end of a character, because T, N, K, L, E and R all do both. My best guess is that that character is R, because it never appears as a double, and there are no lines that consist entirely of Rs, and because R is never followed by an I.