Minor pentatonic, Blues, Major pentatonic, Minor and Mixolydian
The Eric Johnson-esque bits are normally minor pentatonic runs across positions occasionally with extras notes from one of the above scales thrown in. Also notice a lot of ascending arpegio's and decending sequenced scale pattens normally in an odd number grouping (often groups of 5).
Given that Joe always professes to be a feel player I wonder how much theory thought actually goes into it. However that seems to be it in more or less what he plays in a nutshell.
Hope it helps.
PS. Playing Joe's stuff does comes with time, technique development and practice but what always fascinates me is that his playing is almost always improvised with only one or two takes to get the recording down. I'm truly in awe of that level of improvisational skill.