Hey - I SO there! I spent over 20 years just noodling in the standard pentatonic boxes and thinking that I never needed to know any of that theory guff.
Recently though, I have started taking lessons with a great teacher, and he has really opened my eyes by showing me 'modes' and switching between major and minor pentatonics during a solo. Also, he is making me learn the exact notes on EVERY spot on the fretboard. Previously I knew the notes on all strings within the first 5 frets OK, but after that I never bothered to learn the others so he is familiarising me with ALL the notes from the 6th to the 11th frets as well so I can land on ANY fret on ANY string and immediately call out the note - boy that opens the mind a little bit too.
He is also now taking me through triads and building solos from those - very very exciting, and it is really breaking me out of the 'boxes' that I was trapped in before, plus making my solos much more melodic rather than just 'lick bashing'.
Here is a quick Bonamassa lesson (via GuitarEdge mag) where Joe talks about using modes to move around the fretboard:
http://www.youtube.com/watch?v=P6ZCgcsTiCM
Strangely, according to my teacher, a lot of the older players were doing these things back in the 50's and 60's without really knowing the theory behind it. They just had a natural instinct for it I guess.
I am so glad I am learning this stuff now though - it is really opening up how music is strangely matched to mathematics, in that there are certain mysterious 'formulas' that apply that can do wonderful things...
Best of luck with your learning!
JBLP Gold Top #129 - redubbed "#1 in Oz"