Aside from the PMenu article:
Ross Enamait has a good piece about how he went about building some additional muscle.
From a quick glance over your log, you are doing some pretty tough bodyweight workouts, but are somewhat lacking in barbell strength. My suggestion would be to specialize a bit in some of the barbell lifts for the upper body for a while, or at least rotate them in on a more frequent basis. By "barbell" I really mean "weights", since dumbbells or kettlebells might be as good an option as well.
In addition, if the stimulus is there, then the calories might not be. There are very few situations you can gain muscle on a calorie deficit, and almost all of them deal with situations where you are grossly obese or really out of shape, neither of which you seem to be.