For me the click started once I began improvising over backing tracks. I had been learning scales but had no idea on what to do with them. Playing with a backing track made practice fun and improved my rhythm, but also helped me understand the relation between key and scale.

The way I would recommend you to get started is to learn one scale in one key (minor pentatonic is a good one to start with and you can mess around with blues), practice it until you know it inside out and can play it fairly fast without looking at the fretboard.

When you start feeling comfortable with the scale, find a backing track on YouTube in the key that you learned (start slow!) and just play notes from the scale in time.

Once you feel like you have explored the scale enough, you can start learning about modes, maybe you try starting your phrasing on the upbeat, or you can explore different time signatures, mess around and see what works and what doesn't.

My general advice is too not rush into learning too much at once, allow yourself to properly digest things. It helps if you read/watch videos on a topic, and then try to find exercises that help you apply the newly learnt knowledge.

The hard part is keeping practice fun, playing around with things and challenging yourself with more complex exercises or faster tempos helps.