Reading the Data

SetDirectory["/home/faculty/struther/public_html/Courses/5903/Decryption"]
PlainTextBig=ToLowerCase[Import["ATaleOfTwoCities.txt"]];
PlainText=StringCases[PlainTextBig,{LetterCharacter,Whitespace->" "}];
PlainText=Drop[PlainText,-1];
Short[PlainText,30]

Counting Characters in the File.

In alphabetical and count order.

Tallies=Tally[PlainText];
TableForm[Sort[Tallies]]
TableForm[Sort[ Map[Reverse,Tallies]]]
Length[PlainText]

OK so there are two "funny" caharcters in the text.  I have no idea what they are. I am going to delete them.

NewPlainText=DeleteCases[PlainText,"é"];
Length[PlainText]-Length[NewPlainText]

Got them!  Now to split into 5 (Why five?  Why not!) pieces and make an appropriate number of  alphabets.

NumberOfAlphabets=5;
SplitPlainText=Transpose[Partition[NewPlainText,NumberOfAlphabets]];
Alphabet=Join[CharacterRange["a","z"],{" "}];
NewAlphabets =Table[RandomSample[Alphabet,27],{NumberOfAlphabets}];
Subs=Table[
MapThread[Rule, {Alphabet, NewAlphabets[[i]]}],
{i,NumberOfAlphabets}]
UnSubs=Table[
MapThread[Rule, {NewAlphabets[[i]],Alphabet}],
{i,NumberOfAlphabets}]

Encrypted=StringJoin[
Flatten[
Transpose[
Table[
SplitPlainText[[i]]/.Subs[[i]],
{i,3}]
]
]
];
Export["Encrypt.txt",Encrypted]