What has worked for me is to have them learn this grid (I call it "the musical alphabet")
A-A#(Bb)-B-C-C#(Db)-D-D#(Eb)-E-F-F#(Gb)-G-G#(Ab)-A
I explain to them that for our purposes there are 1/2 steps between E-F and B-C (that takes away the Cb and Fb that may be confusing at first). I explain to them that as we are going up in pitch (toward the bass body) we are going forward in the alphabet and as we're going down in pitch we are going backwards. I then have them play and call the notes on each string up to the 12th fret with #s going up and flats going down. We then look at from the 12th fret up and I explain to them that it's the same pattern as the bottom 12 frets. It's pretty effective.
Yea, that he knows. Maybe I'm not explaining this like I should. It's like he's afraid to venture out past root whacker land for fear of causing a train wreck. When I try to get him to explore during a tune, if he hits a sour note, he goes right back to root whacking. Ive taught him notes, intervals, scales and modes, basic sight reading. Now I'm trying to tie it all together for him, but I think he is afraid to "venture out" because of fear of the "wrong note" and sounding bad. When it's all laid out for him, he does ok. Not great, but ok. So could transcribing (from other instruments) get him out of his fear? If so, I might need to refer him to someone more skilled at that than I am. Or maybe he just needs to keep plugging away until it sinks in?