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The Input of http://pastebin.com/F9ZDQZYC is: "THE EYES ARE USELESS WHEN THE MIND IS BLIND".
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I've studied Code #2 a little bit more after I made it and discovered a few things about it that will hopefully make it easier for you to understand.
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Code #3 is like Code #1 but you're now able to use multiple instances of the same letter and its output varies.
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Our input will be: "HELLO WORLD" and we'll encode one word at a time.
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Code #2 & 3 are a lot less picky than Code #1.
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To understand Code #2, it'd be best if you already understood how the Vigenere Cipher works.
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HELLO is 5 characters long, meaning we need to make a 5x5 square & fill in the alphabet.
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	1	2	3	4	5
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There are 5 different groups of letters:
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1	A	B	C	D	E
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2	F	G	H	I	J
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1: UCSD
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3	K	L	M	N	O
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2: QBVGLP
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4	P	Q	R	S	T
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3: YJNRZT
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5	U	V	W	X	Y
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4: AMFKWX
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5: EIHO
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Since we've filled the whole 5x5 square with most of the alphabet(A-Y), the "Z" will be apart of the next group(A) of 5x5 squares.
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The reason why I chose for the letters to be in those specific groups/order is irrelevant now, so all you need to make note of is that for this code, the letters are in that arrangment.
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------------1st GROUP has no Group letter------------
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	1	2	3	4	5
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Now we just create a vigenere table with these letters:
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1	A	B	C	D	E
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2	F	G	H	I	J
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The first column will just be the regular alphabet in order, (A-Z), and the 2nd column will be next instance of that particular row/group.
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3	K	L	M	N	O
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4	P	Q	R	S	T
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For example:
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5	U	V	W	X	Y
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------------2nd Group will be defined by "A"------------
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1st column up to 5 letters:
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	1	2	3	4	5
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1
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1	Z	_	_	_	_
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A
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2	_	_	_	_	_
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B
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3	_	_	_	_	_
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C
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4	_	_	_	_	_
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D
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5	_	_	_	_	_
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E
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1st & 2nd column up to 5 letters:
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Our output will now have a padding of "X"'s, and it will be as long as how many spots are in the group (in this case, 5x5=25)
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1	2
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XXXXXXXXXXXXXXXXXXXXXXXXX
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A	M
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B	V
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C	S
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Just like Code #1, Knowing the number form of letters, A=1,B=2,C=3...Z=26, We now place the order letter in the position of the letter's number.
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D	U
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E	I
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(H)ELLO		XXXXXXX1XXXXXXXXXXXXXXXXX
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Because:
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If our first letter happened to be "Z", then we would know that "Z" is apart of GROUP A, BUT is in the 1st postion in the 5x5 grid, meaning:
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Row A is apart of this group: AMFKWX
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Our Z, (1st character being encoded: Order number = 1), would be in the 1st postion of our output:
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ROW B is apart of this group: QBVGLP
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ROW C is apart of this group: UCSD
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(Z)ello		(X)XXXXXXXXXXXXXXXXXXXXXXXX
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ROW D is apart of this group: UCSD
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ROW E is apart of this group: EIHO
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(Z)ello		(1)XXXXXXXXXXXXXXXXXXXXXXXX
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Meaning:
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Since "Z" is in Group A, we need to show that in your output by adding ".A" after the "1":
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Columns & Rows 1-5 would be:
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(Z)ello		(1.A)XXXXXXXXXXXXXXXXXXXXXXXX
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1	2	3	4	5
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A	M	F	K	W
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and it would look like this:
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B	V	G	L	P
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C	S	D	U	C
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(Z)ello		1.AXXXXXXXXXXXXXXXXXXXXXXXX
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D	U	S	D	U
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E	I	H	O	E
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Now back to our actual input: H(E)LLO
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You would do this for the 26 columns and 26 rows thus making a vigenere table using these letter configurations.
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H(E)LLO		XXXX2XX1XXXXXXXXXXXXXXXXX
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HE(L)LO		XXXX2XX1XXX3XXXXXXXXXXXXX
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So if we have an input of: TEST CODE
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We encode by finding (T)EST on the top row of the vigenere table and the T(E)ST on the Left most column and find the intersection between the two, which would be: O
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Now we have a 2nd instance of the same letter (two L's), All we do to show that multple letters are apart of that position is add a "|" between them:
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Continue to do this process until the last letter of the word:
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HEL(L)O		XXXX2XX1XXX3|4XXXXXXXXXXXXX
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TEST = OST
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HELL(O)		XXXX2XX1XXX3|4XX5XXXXXXXXXX
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For the last letter, you find TES(T) on the top row and (T)EST on the left most column, which would be: Y
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and if we had to encode a letter from a different group, same rules apply. 
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Now continue this process for the rest of the input, TEST CODE, and it will leave you an output of: OSTY ICOC
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If you find it a bit hard to understand when trying to decode, space out the columns:
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Final:
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HELLO = XXXX2XX1XXX3|4XX5XXXXXXXXXX
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Final with 25 columns spaced out:
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HELLO = X	X	X	X	2	X	X	1	X	X	X	3|4	X	X	5	X	X	X	X	X	X	X	X	X	X
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To save time, Here is how the rest of the input would look:
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HELLO WORLD:
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XXXX2XX1XXX3|4XX5XXXXXXXXXX
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XXX5XXXXXXX4XX2XX3XXXX1XXX
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Essentially, you can also do the same thing as Code #1 and repeat the numbers if you wanted to:
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HELLO WORLD:
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222221113333|45552222222222
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55554444444422233311111555
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That's all there is to this code. :D
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Thanks for participating for Code #1! :D
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 - DWC