Ok, so I recently started going some cryptography in my spare time after entering a YouTube competition. After a few hours, I finally caught on the way to step-by step solve the puzzles. For this particular puzzle, I got the hint to use frequency analysis from the previous puzzle. Instead of taking a trip down the tedious path and going through and looking at the repetition of each letter and word pattern, I used this handy little website. http://www.richkni.co.uk/php/crypta/freq.php To compliment me with switching letters back and forth, I used http://25yearsofprogramming.com/fun/ciphers.htm which also contains a "FA", but makes it much easier to replace letters and see immediate results. (I always compare frequency in the text to frequency in theory and try to match them.)
The following is an example I use to step my way to more efficiently cracking the code; efficiency is everything. This gave me the vital letter frequency, as well as 2,3,4,5 and 6 letter repetitions! I immediately looked at the 3 letter repetition section to notice "qao". I automatically assumed this to be the word "the", as it is many times. Now that I have those three letters, I apply this to the six letter section in hope to get something out. The "goqqon" word gets my attention because it contains two pairs of like letters. Also because we know that o=e, it significantly helps. Now, I thought to myself in the context of the previous two puzzles, 'what could _eXXe_' be? (with XX being a double letter). It didn't take long for me to think of 'letter'!! I also noticed that it was able to be plurals, so I added an 's'. From here, things got slightly easier. With the help of frequency analysis, I tried to strip the less common letters and replace them with more popular ones, and sometimes with luck. Research in word patterns I thought benefited me hugely, and so I recommend them too; http://scottbryce.com/cryptograms/stats.htm.
I started strongly from around the centre of the puzzle, with "ALL THE LETTERS IN A MESSAGE IS THAT" and then slowly edged my way to find smaller words in between that made things clearer. As I write my 'confirmed' (used) letters down on paper, I have a remaining list which can still be rearranged anywhere without affecting the already made words. This is really good for times when you are stuck, (as I was). You can simply change a few letters and hopefully see a pattern that makes you think. Sometimes you can try to fill in the sentence with your own words also. e.g "THIS IS CALLED A _____ _____". I knew from the context that the puzzle was referring to another cipher (which also gave away the word 'cipher') but quickly researched a few cipher names to reveal a nice fit of 'vigenere'. The other tricky part was arranging the less common letters. However, sometimes the surrounding letters gives it away, such as "freQuency". Also, when you have words already made, spacing them helps significantly.
THE LAST MESSAGE WAS ENCRYPTED USING AN AFFINE CIPHER AT (OQBTOZCTOIIE) MOVING ON NINE LETTERS EACH TIME. THE PROBLEM WITH JUST USING ONE CIPHER TO ENCRYPT ALL THE LETTERS IN A MESSAGE IS THAT WE MAINTAIN THE FREQUENCY OF LETTERS IN THE PLAIN TEXT SO WE'RE ABLE TO USE FREQUENCY ANALYSIS TO HELP DECIPHER IT. WE COULD INSTEAD USE DIFFERENT ALPHABETS FOR DIFFERENT PARTS OF A MESSAGE, FOR EXAMPLE WE COULD ENCRYPT THE ODD LETTERS WITH ONE CIPHER AND THE EVEN LETTERS WITH ANOTHER. THIS IS CALLED A VIGENERE CIPHER WITH KEYWORD LENGTH TWO GOODLUCK!