I feel like I'm in the same situation. My theory and notes knowledge is nowhere near where it should be given the amount of time I've been playing.
Id say as far as music theory goes, I think I've got it down, I'm rusty because of the amount of time I haven't been looking at anything music related, but even today I found its coming back pretty quick. My issue is not know where what notes are where on a fretboard. I was never a piano player, so I can't even really use key knowledge and bump it up against a fretboard either... I know where Middle C is on a keyboard, that's about it, lol.
The Guitar Grimoire book I bought will definitely help I think, it has every scale imaginable, patterns, modes, etc, and even shows the scale on a keyboard as well.
The main tip is really mostly practice.
The notes on a guitar repeat (the open e, is also found on the b string 5th fret, third string 9th fret, fourth string 14th fret, and so on) so one practice technique is to play the same line (same octave) of music at different positions of the neck. Another is to play the same line of music on each string but using only one string at a time.
Sergio's suggestion about the modes also helps as you visual have an idea of what notes are available for a certain key at a certain place on the neck.
Just before I posted my last post I picked up my daughters beginner guitar book, I feel kinda silly playing Ode to Joy and Mary had a Little Lamb, but I've been doing it thinking more along the terms of what Les suggested, just going through saying the notes out loud.
While I'm learning notes, I'm also being required to learn more chords. I recently signed up for Guitars for Vets, and my instructor is really pushing for me to learn and memorize more than the "core chords" everyone learns in the beginning (C, G, Em, Am, D).... at least I have someone pushing me to get it done though.
I think all these suggestions will help out, so thank you everyone
Hopefully ill have it down in a week or so, lol, just wish I would have done this 20 years ago instead of going the easy route and following Tabs.