Slipin -
I'll definitely check out that fretboard trainer. I find myself wishing I could limit the GT trainer to a specific region of the fretboard where I have trouble.
Yep, the ultimate goal should be instant recognition. It's like kids learning math facts - repetition to develop instant recognition.
I can see saying the note as you are playing it will help. When I did the lesson on the solo for Day Tripper, the instructor said "OK, we are going to start on a B and we'll get that here on the D string." Just because he said that, that is now one of the notes I can instantly recognize. If he just said "OK, the D string on the 9th fret", that would not have happened.