Try to rise above thinking solely about the mechanics of what you're doing (ie, scales, arpeggios, modes) and think in terms of melody and how to convey emotion in what you're playing.
I get so many students stuck in this rut of knowing all the scales inside out, and then when they go to play a solo, all they can do is edit a bunch of scales together.
The 'theory' stuff is great for learning guitar, practicing and keeping your fingers nimble.
But when you play music, you have to use the knowledge you've learned without sounding like you're doing things 'step by step.