It seems that you might have two problems. First is just being able to insert the patterns in the right change, and second is divorcing yourself from playing the pattern.
Here's what I would do....
1) Work out some patterns you like, and practice playing them throughout some tunes REALLY slowly. (As for tune suggestions... I don't know what you're into, but my favorites for practice are "All The Things," "Blue In Green," and "Solar" All provide many changes to play, but aren't as convoluted as, say, Giant Steps.) Increase the tempo as you become more comfortable. There's no use in trying to play more note based if you can't iron out what notes work with what change, so solve this problem first. Patterns are a good way to map out groups of correct notes in a way that organizes them into something coherent and musical.
2) Once you commit these patterns to memory, then you also understand what notes you can play on each change. Cease to think of patterns as patterns but as pools of notes you can use to make new lines. Again, practice REALLY slowly at first. Also, what I said above I think applies to this step. It's all a process of trial-and-error from this point on. The more you experiment, the faster you will attain the goal of freeing yourself from patterns.
I like to think of this Bill Evans quote when practicing vocabulary:
"First of all, I never strive for identity. That's something that just has happened automatically as a result, I think, of just putting things together, tearing things apart and putting it together my own way, and somehow I guess the individual comes through eventually."
Really, all it boils down to is 'putting things together, tearing things apart and putting it together' in your own way. Easier said than done, for sure. But for the past year or so this is all i've been doing, and I think my lines have become more controlled as a result... That said, it never ends... there's always room for more... but you'll reach a point where you'll be thinking and playing differently.
Best of luck... Keep at it... hope this helps.