I am on Alphabet 3 and still not seeing a connection with the light accents on the words as to when to use them and when not. For instance, most of them have the accents but not the words buuj and juub, or kuub or buuk. Am I missing where this is explained?
When there is a waw (W sound), it becomes uu in the middle of a word. So they don't put accents because it is already understood to be connected with uu. I hope you can understand what I mean. Besides this, you may find this with the letter yaa (y sound) as well where it is in the middle connecting two letters and is understood to make the ee sound.
I believe you're right - I learned Dutch as a child and English just a short while later and for me I can "hear" something is not right in the construction of a sentence, but can't always explain why. Your ear (and your eyes) get attuned to the language with time. I'm only on week two of learning Arabic (I wanted a challenge outside of the usual alphabet) and find that repetition is the only way to learn at this point in my life.