My #1 suggestion would be interval training.
Having scales under your fingertips isn't much use, unless you can correlate that information to the twists and turns of the musical phrases that you're trying to communicate. This relates directly to Fergie's suggestion vis-a-vis the Jeff Berlin materials.
The best thing that ever happened to me in terms of improvisation, learning new parts, fretboard navigation, etc., was having my dad teach me about tetrachords and intervals, then having that backed up by a college course that concentrated on hearing, singing, reading and playing intervals.
As with any learning process, the more senses you can engage, the better. Mix receptive and expressive processes. Have him listen to different styles of music, and talk about the intervallic choices that define its character. Talk about the moods that intervals invoke, and how that depends on context. Sing or play intervals, and have him identify them. Call them out, and have him sing them back to you. Repeat the process, but put a bass in his hand, and have him play them back to you. Have him study them on a piano keyboard, just to give him a different visual reference. If he's a reader, teach him how to identify the various intervals by the number of lines and spaces between adjacent notes. Have him build chords by stacking intervals...
The more of these types of exercises the two of you can come up with, the faster this stuff will be rutted into his nervous system.
One other thing: What's his motivation like? Are you force-feeding him, or is he actively seeking to learn the fingerboard himself? Sometimes, you need to address attitude issues before you can move forward with the mechanics of playing. This is his problem, and he needs to be engaged in his own learning process. If you're able to challenge him to come up with his own exercises and strategies to solve the problem, it will reap major dividends.