| It all boils down to transcription. You have to think of anything you're trying to learn musically as you would do learning a language. it's all about vocabulary, phrasing, time, space, statements, answers, and so on.
If you were to hear "¿Hola. Como Esatas?" on a daily basis at a certain point of social interaction, you would soon learn that it meant "Hello. How are you?". Just as you did when you were a child and your parents were constantly talking around you, you picked things up because they were repeated over and over again. Now as young, middle aged, or older adults we don't have quite the sponge like capacity as we did when we were children, but with some persistence and hard work you can train your musical ear to work the same way your language ear works.
Start listening to records that have phrases, solos, and general language that you're interested in learning. Then figure out what those notes are, and what the harmony is behind them. Notate these solos, phrases and anything it is that you want to soak up, and then work on transferring these ideas to your instrument. Start simple with short phrases at slow tempos and get a feel for the phrasing of whomever you're transcribing. Try to get inside this persons time, phrasing and ideas to get as much out of the transcription as possible.
There are of course exercises that utilize triads, chromatic approach notes and a number of other ideas. I still use these things today to keep myself in shape. But the real learning point is in transcription, learning from a master of the artform, and then taking what you learn from them and using it to form a unique voice of your own.
Go as far back in the history of the music as you can and give yourself the grounding and understanding of what has come before you in the story of improvised music. If you can start out with Fats Waller, jellyroll morton, art tatum, louis armstrong, king oliver, lester young, dexter gordon, charlie Parker, Miles Davis, art blakey, wayne shorter, herbie hancock, chick corea, pat metheny, michael brecker, brad mehldau... and as many people who you dig that you can learn something from.
I would stop trying to apply theory to improvisation, and do what the term improvisation alludes to... which is creating something new out of virtually nothing, and in a organic sense, not an applied theory sense.
In transcribing you will come across every theoretical exercise and pattern known to mankind...... far better for you to have come across this without having to think about it, and then committing it to your subconscious so it will never interrupt your creative thought process as you go about improvising.
Easy,
Janek | 
