I've never actually studied theory on the guitar but have developed an understanding of musical architecture mainly by ear. Practicing diatonic runs and homemade exercises as you explained above opens up the fretboard and helped me to 'feel' the notes I want to play at any position on the fretboard. I've always approached composition a bit differently, I just imagine what I want to play first and then work it out - as opposed to approaching it theoretically. So when it comes to playing runs and licks, I hear them in my mind first, then work them out, then practice playing them over and over.
For a long time I used to try creating lead around scale shapes but found that I only started creating new sounds when I got away from 'shape mentality'. I was always terrible at maths in school and college and I find theory a bit like studying maths. On the other hand I was good at art so a looser more creative approach work better for me.
My take in the August assignment was an example of a solo constructed in one sitting (section by section) - I listened to the backing music and imagined what I wanted to hear over it, then worked it out.
As far as vocals on my other stuff goes, I'm working on church choirs along with symphonic elements. The plan is to also mix in techno sounds and robotic voices along with human voice - from regular through to death metal growls. I'm trying to stay away from sounding like a band with a regular singer. It's a major undertaking as far as midi programming goes but it's starting to come together.... slowly!
Thanks again for the comments!