One of the hardest things to do when playing over changes is phrase well through the chords. In order to do this successfully we need a few things in our playing bag of tricks. The first is an excellent fretboard knowledge. Without this you stand no chance of hearing and finding your way through the changes and you'll get lost all the time preventing you from phrasing effectively.
The second aspect is being confident enough to phrase properly through the changes and have a thread in your improvisation. You can't rely on your personal array of 'licks' to get you through as the scales are changing so rapidly that these will no longer be effective.
The first problem is the easiest to solve. Learning the fretboard is on of those things that you simply have to get on with. Doing continuous scale exercises over changes and learning your modes all over the fretboard takes a long time but frees you up immensely in the long run. I will do a tutorial on fretboard visualisation in a broad context in the future.
The second problem is harder but there are ways to help. One way we'll explore here is motivic development.
I'm going to show you how to take a small melodic idea and mold it through a set of changes, only changing the notes required to fit the phrase to the new chord/scale. Over the coming videos I'll transcribe a few improvised motivic solos which you can check out and analyse. Try this approach for yourself. It's a great way to develop a thread through your improvisations.