I understand your confusion. It isn't that you don't understand the word "miss." I think it is just that in English, the simple past tense can be used at any time. So, you can say, "I missed you" in the same place that you would say, "I had missed you," and you can use it in the same place that you would say, "I have missed you." (But you can't use "I had missed you" and "I have missed you" interchangeably.) Hope that helps. It's kind of confusing! The simple past tense is more versatile than some other languages.

It should be "Before you came into my life I missed you so badly" as you need an adverb to tell you much the person was missed. The sentence is a contradiction, because how can you miss a person you haven't even met? Still, that is called poetic licence. Song writers write lyrics to fit the music.

I had missed you = a finished process in the past. It is not finished, so no past perfect. BTW, when connecting sentences with "before" you always use the past tense. The past perfect also happens to be the past tense to the present perfect. From there you can see that "I had missed you" is just not correct.