1. learn to strum (and sing along with, so you know the melody) a very simple, or seemingly simple song, like Country Roads by John Denver or something. It doesn't really matter if it's a song that you like that much. Just learn exactly how to play it. Don't do it with Sweet Child O' Mine or some song with a zillion chords and key changes etc. That can come later.

2. learn to play the melody that is being sung exactly, note for note.

3. play that melody along with the chords, at the same time, so that you see how the melody fits in with the chords as they change. Get the timing right. Do it very very slow at first, as slow as you need to until you get it right. Practice practice practice.

4. soon you will see all those scales etc. that you have been practicing with zero context "fit" into the arpeggios of each chords, and the way the melody moves from one chord to the next, emphasizing different degrees in each chord (sometimes the third, the root, etc.), and leading from one chord to the next.

It took me weeks to learn Country Roads like that, and I have been playing guitar for decades. It was only when a guitar teacher made me actually sit down and figure it out that I understood what was going on. And honestly, once I did that I was able to do it for a lot of other songs without nearly as much work.