I learned guitar by myself 3 years ago by just noodling around and using the internet for tabs. Basically, the only reason I wanted to start playing guitar was I liked guitar solos.
Consequentely, I'm good at guitar solos and lead...but absolutely crap at chords and rhythm! Everybody says that I'm very strange that way. I can't remember any chords, my fingers can't reach to hit certain chords, and I can't make chord changes fast enough for any decent song...but I can do pentatonic on the fly and do chromatic scales pretty quickly. I have no musical background but the way I learned was I got tabs of the guitar solos I liked and just played them and messed around until one day, I noticed they shared many of the same notes and lo and behold, I had discovered a scale by accident. Then I just remembered the notes to those guitar solos and I found I could improvise by just remembering those notes.
Then I loaded a backing track and drums that were in a certain scale and let it go and I'd just play randomly and improvise on the fly. Sometimes I'd just play something in a certain scale and loop it, and then I'd have my own backing track and then play over top of it. One really good way is to find a slow/jamming song that you really like. Something emotional like Purple Rain. It's a good song to just play any kind of lead randomly on and it will fit because the tempo is always steady. That's all I would do for hours. I'd always have a guitar in my hand the entire night nomatter where I was or what I was doing. If I'm watching TV, I'll have a guitar...and I'd just be picking individual notes (I get bored with chords - maybe it's because I don't know any) and trying to match the scale of whatever I was playing to anything that comes on TV, etc.
Want to know the most embarrassing thing? The guitar solos which were the first music I ever taught myself on guitar (EVEN BEFORE THE C CHORD!!!) were the solos in:
Olivia Newton John - Let's Get Physical (This taught me more scales than anything since it moves from one end of the guitar all the way down to the other and back again).
Whitesnake - Love Ain't No Stranger
Journey - Who's Crying Now
Poison - Ride the Wind
Law and Order Theme - (Yes it DOES have a guitar solo in the full version of the song which is like 5 minutes long and never broadcast on TV anymore)
I probably am in the exact reverse situation as you. I need to find a real guitar teacher to teach me how to actually play guitar as in chords and rhythm. So basically my advice is that I think the box is that you are trying to be too technical and remembering everything...you just have to play until you feel the notes in muscle memory and you can hear them so you know where to put your fingers next to get that right note that goes with what you are playing. Best advice is to put on a slow backing track in a certain key, and then just play notes until you find out the notes that fit that key and then keep playing them and noodling and improvising. Nothing more rewarding and enducational to me, as a (totally crappy) guitar player, than to slow jam some searing notes with distortion to a cheesy mellow backing track like you were making the soundtrack to an 80s Chuck Norris movie.
Here's a el-cheapo backing track I made awhile back that I find works quite well to play along to. It's the same short sequence (you might need to edit it in some software to get it to loop longer) so you have to really put out some good long sustaining notes or fast picking to stave off boredom...but if you get it, it can sound amazing.
http://ng.jeremy.googlepages.com/jeremybacking.mp3
It sounds well with these scales:

Basically I have that memorized and I find it works with lots of songs and if the song is in a key that is higher or lower, I can just transpose it up or down a few frets but the pattern remains.