Identifying the Encryption
I put the encrypted text in this site to identify the encryption type. The first 2 possible options that popped up were "NATO Phonetic Alphabet" and "Tap Code Cipher". The former did not look appealing as the problem clearly gave options like C=K and Y=Z, but it didn't have any extra options. So, I checked the latter. This one seemed interesting. I googled what this tap code is and Wikipedia said Tap code is also known as "knock code", which matches the title "AlphabetKnock Code".
A brief Note on how Tap Code works
I won't be going in detail how this works; you can check the Wikipedia for that. 
In a 5x5 grid, for A, it will be ". ." (1 dot 1 dot) and for B, it will be ". .." (1 dot 2 dots) and for C, it will be ". ..." (1 dot 3 dots) and so on.
Solution
If you utilise the hint, you will find "4x6", which suggests it is a 4x6 grid which equals 24 characters. The other 2 characters are C=K and Y=Z. In short, we have to assume which character it will be based on the context (or flag). By now, you should already get the flag. The only odd thing about the flag is that there is one certain character which is out of place. You just need to replace that to get a meaningful flag.
There are square grids all over the internet, but no 4x6 grid. So, you have to do it manually. But if you want to automate it you can do it like this:
You are basically utilising 6x6 grid, but you have to assume the last 2 rows are not there. After all, the the flag doesn't use the last 2 rows. So, you have to fill them with any other distinct random characters or numbers or whatever.