I want to really understand the guitar.

I know exactly where you're coming from. I took guitar lessons for a little over a year. My background was playing bass by ear for years. I wanted to learn guitar and improve my bass playing at the same time. I quickly figured out that what I needed was music theory and guitar was just as good a tool as any. Fortunately, I my teacher was able to adapt to my needs and focus less on getting down eight and sixteenth notes. Go spend some time at a big chain bookstore in the music book section. Look at all the guitar books. At least one will grab you. Look for something that'll teach you the fretboard and some theory in a way that makes sense to you. You already know all the notes, so you should be able to pick that part up rather quickly. And, of course, it all starts over again at the 12th fret. You're correct in that you don't need to learn 4820 chords and learning the chord formula is more likely to help you. You may find something like http://www.amazon.com/exec/obidos/ASIN/0964863219/metafilter-20/ref=nosim/ helpful. It'll help you learn how the various chords are constructed and it's a workbook in the classic grade school sense. I have it and a few others by the same author. It's also worth learning all the keys and modes because they will help you understand how to solo as well as how all the keys/notes relate to each other. Knowing the modes will help you understand how to play a scale (mode) over the entire neck. As for the jazz theory, again, I recommend some face time with as many books as you can see. http://www.amazon.com/exec/obidos/ASIN/073902406X/metafilter-20/ref=nosim/ seems well received by fellow amateurs. Also, if you're not already on the various guitar forums, do some digging! There are lots and lots of people out there who are more than happy to help you along. And don't forget Youtube and lots of other video sharing sites have guitar lessons.

Two things that IMHO can really help someone develop as a player: 1. record yourself and listen to it 2. arrange songs for the guitar that were written for some other instrument

You might already know this since you have some music theory under your belt, but understanding basic music harmonic behaviours like http://en.wikipedia.org/wiki/Voice_leading, http://en.wikipedia.org/wiki/Tonicization, http://en.wikipedia.org/wiki/Inversion_(music)#Inverted_chordsand how they affect music can help you be a more flexible and adaptable player of any instrument. Do exercises of different types. Rhythm exercises are often ignored by guitarists, but I think strumming, picking, or even just tapping different rhythms can be useful. Try playing a scale in quavers, change half way to triplets, then change back to quavers. Play with accents on different parts of the beat. Choose a different time signature and tap a rhythm. Play around with http://en.wikipedia.org/wiki/Hemiola in rhythm. Once you have a grasp of these, you'll ear them in music you listen to, and find it gives you a bit of flexibility in playing. If you always play with a pick and find yourself in a rut, put the pick down, strum with your fingers, or do finger pluck style, I find it makes the other part of my brain work a bit harder. Alternatively, if you always play plucking with your fingers, get a pick and try that. I agree with ludwig_van that writing scales, rhythms, chords etc on a musical staff will help your musicianship. If (like me) your musical notation looks like a chicken has dipped its feet in ink and walked over the paper (a quote from my composition lecturer) then a simple notation program like anvil studio or finale notepad might be better :)

I'm a guitar teacher. Read http://ask.metafilter.com/95962/Help-me-become-a-real-Guitar-Hero#1401297 to this http://ask.metafilter.com/95962/Help-me-become-a-real-Guitar-Hero. I'll emphasize that to supplement your scale/chord practice on the guitar, you should write those chords and scales out on the staff with a pencil and paper. You should also sing them and play them on the piano. All of these things will go much further than just playing them on the guitar -- similarly to the distinction you draw, I'd say this stuff is the difference between "someone who plays guitar" and "musician."

Heres something that made a huge difference to me. I had guitar lessons, I was studying music at uni, in bands and I thought I was pretty damn awesome at the guitar. So I was having classical lessons, and my teacher asked me to play G Major one octave. No sweat. 2 Octaves. No worries. 3 octaves... ummmm what? I thought I knew G major (and harmonic/melodic minor etc) but I'd been playing them two octaves (e.g. G major, starting third fret of the bottom e string, finishing 3rd fret of the top e string). When I learnt to stretch it to 3 octaves on the guitar it opened me up to whole new patterns, finger movements. You might already be all over 3 octave scales, but if not, give it a go. Another thing that helped when it came to modes was to just try them. At first my fingers didn't know where to go, what felt natural etc, but after a while I started to find patterns I liked the sound of, my fingers got used to the shape of the mode and I was away. Another thing I do when I'm in a rut is listen to music from a totally different style than I am used to, or try to play music from a style I'd never normally attempt (even if I don't like it). So maybe take a few tacky Europe songs, or Britney Spears, or just something different to your normal style.

http://www.berkleeshares.com/guitar You'll find a wealth of free downloads here.

For me practising is half of it. The other half is improvising with other musicians. You need to not only know how to make music on your own, but learn how to be involved in a conversation with others. It is much easier to improvise when there is someone reacting to what you do, extending it, supporting it, etc. You will learn from their ideas, and learn all kinds of subtle things about playing music that you don't get from practicing alone, such as hearing the breathing of another player, the tapping of their feet, their expression and body language. These things communicate so much of the overall experience, and give you an indication of how they have internalized their music. And, don't forget about time. Probably the most important thing of all, more than chords & melody, is the feel with which you play. This is another thing that you need to do with other musicians, not just alone (in addition to practising with a metronome by yourself of course). A good swing feel is an indefinable, un-notatable thing. Try to play with the best drummer and bass player (or just bass player) that you can find. Listen to http://en.wikipedia.org/wiki/Kind_of_Blue (wow, 50 years old next month!), e.g., and don't just notice the effortlessness of the playing, but how few notes there often are, and how good things just feel. Miles plays his notes like you would arrange jewels in a display case. Each one delicately placed and glittering, lots of space around it, because it takes up so much room all by itself.

If you are familiar with http://www.youtube.com/results?search_query=Tuck+Andress&search_type=&aq=f of Tuck & Patti, you might be interested in http://www.tuckandpatti.com/tuckscorner.shtml he has done and is continuing. But ultimately, for many styles, you can't make the mistake of putting all your energy into left hand development. To get http://www.youtube.com/results?search_query=Stanley+Jordan&search_type=&aq=f fluidity, you are going to have to learn hammer style, including how to http://www.youtube.com/watch?v=fMnjnIOM2fQ and http://www.cyberfret.com/techniques/hammer-ons-pull-offs/index.php forcefully. And while it is great that you are working on learning scales and want to be able to "know" the position of every note, instantly, on the fretboard, you'll find this a much more daunting task, once you start investigating the world of alternate and open tunings, which make http://www.youtube.com/results?search_query=John+Renbourn&search_type=&aq=f acoustic music so interesting. You also need to know how to get rhythmic power and accent out of your guitar, by close coordination of left and right hand technique, including playing into partly and fully damped strings, using harmonics, and being able to finger pick, in various styles and patterns, including claw, roll, and Travis picking. Some of this stuff is 10x easier to learn from a teacher, but given the Internet's resources, if you're diligent, you can find a lot of good tutorial material online. A subscription to http://www.guitarplayer.com/, as well as frequenting their Web site for articles and tutorials is one good place to start your search.

You have a high level question you have to answer for yourself - "Are you are willing to put in the hours?" Conventional wisdom (for what it's worth) says it takes 10000 hours to become an expert, in any subject. Let's say you're a genius, and you can do it in half that time. That's still 5000 hours... So, what's it going to be?