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Religous Woes

The sound of the door being opened shakes you from your pondering of the note's meaning, and soon Boris enters the kitchen.
"Oh, hi," he says upon seeing you. "Sorry about not showing up yesterday. It shouldn't happen again - what was bothering me has been resolved."
"Yes, so I gathered," you reply, indicating the note. "I must ask though: why Apollo?"
"Well, being the god of civilization and intellectual pursuits, among other things, he'd be one to enjoy a good puzzle now and then. Thus," he smiles, "a deity after my own mind."

* * *

How, then, do we reach this answer? The first step is to solve the cyphers, either by simply working on them until a solution is found, or by understanding the instructions below the cyphers.
Solving the cyphers, you'll notice that these sentences were encoded in three separate ways:

1. Turn right and left, back and forth, more and more.
Line up the alphabet. For the first letter in a word, you substitute the letter one step to the right. For the second, the letter one step to the left. For the third, the letter two steps to the right. And so on.

2. Half and half, down and to the right, faster and faster, wrap it about.
Line up the alphabet and divide it in half, one line above the other, like so:
ABCDEFGHIJKLM
NOPQRSTUVWXYZ

For the first letter in a word, move one step diagonally down and to the right, wrapping around if necessary, and use that letter instead. For the second letter, two steps down and to the right, and so on.

3. Each kind with their own, then proceed forth at the appropriate pace.
Divide the alphabet into consonants and vowels, like so:
BCDFGHJKLMNPQRSTVWXZ
AEIOUY

Locate your letter and from it move to the right, within its group, a number of steps equal to its position in the word.

This leaves one set of instructions unused… we'll get back to that.

These are the deciphered lines (with sources added):

Believe me, my son, an invisible and subtle essence is the Spirit of the whole universe. That is Reality. That is Atman. THOU ART THAT. -Khandogya Upanishad 6:13:3
God did not give us a spirit of cowardice, but rather a spirit of power and of love and of self-discipline. -Bible 2 Tim 1:7
The Way takes no action, but leaves nothing undone. -Tao Te Ching Ch.37
Now this is my chance to escape his keen eye -From the Zen Koan The First Principle
Blessed are those who mourn, for they shall be comforted. -Bible Matt 5:4
Religion is the opiate of the people. -Karl Marx
Those who wish to change the world According with their desire Cannot succeed -Tao Te Ching Ch.29
When all desires that cling to the heart are surrendered, then a mortal becomes immortal -Katha Upanishad 6:14
Whoever saved a human life should be regarded as though he had saved all mankind. -Qur'an 5:32
A broken mirror never reflects again; fallen flowers never go back to the old branches. -From the Zen Koan Returning to the Ordinary World
My Lord, increase my knowledge. -Qur'an 20:114
All religions begin with a revolt against morality, and perish when morality conquers them. -George Bernard Shaw

The quotes gotten from the cyphers can be arranged in groups of two:

Now this is my chance to escape his keen eye
A broken mirror never reflects again; fallen flowers never go back to the old branches.

When all desires that cling to the heart are surrendered, then a mortal becomes immortal
Believe me, my son, an invisible and subtle essence is the Spirit of the whole universe. That is Reality. That is Atman. THOU ART THAT.

The Way takes no action, but leaves nothing undone.
Those who wish to change the world According with their desire Cannot succeed

My Lord, increase my knowledge.
Whoever saved a human life should be regarded as though he had saved all mankind.

Religion is the opiate of the people.
All religions begin with a revolt against morality, and perish when morality conquers them.

Blessed are those who mourn, for they shall be comforted.
God did not give us a spirit of cowardice, but rather a spirit of power and of love and of self-discipline.

Now is a good time to remember the string of numbers from the note: 28 67 19 19 3 7
Checking the 28th character (including spaces and punctuation) of the quotes from the zen koans reveals that in both cases, it is C. Doing likewise with the other groups, reveals more doubled letters. Now, the two 19s in the string of numbers makes the order of the letters slightly ambigous. I'll go right ahead and reveal, though, that out of the two possibilities, COCMLD is the correct one.

To solve the puzzle, we return to the neglected deciphering rule above: Clockwise spiral, starting up, and follow the right hand guide.
Write the alphabet spiraling clockwise out from A, starting up, like this:
Z
YJKLM
XIBCN
WHADO
VGFEP
UTSRQ

Then locate your letter in this grid, and move one step in accordance with the way the keypad of your keyboard (which should be fairly close to your right hand) is pointing. So, for the first letter, move in the direction of the 1-key (down and left). For the second, in the direction of the 2-key (down). For the fifth, don't move at all.

This gives you the name 'Apollo' and solves the puzzle.

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