how exactly am I supposed to handle the decryption minigame. As far as I have experienced there is no guide to show how it's done
You want to type the big word at the top below the 'TARGET SEQUENCE' text. It'll change, you just keep typing until you fill the progress bar before the timer ends.
I'll try to make this more clear for the next update, sorry it's not very user friendly yet!
EDIT: Update is out and it should make this specific minigame much more user-friendly. If this solution seems to work well, I'll happily apply this style solution to other minigames that are time-based.