I dunno if someone’s already said this or not, because I didn’t read through the whole thread, but the very first thing that came to my mind was–
BUY A METRONOME!!!
Seriously. You are on the best track possible by practicing chords and scales daily. Even virtuosos do that to make themselves even sharper. It’s not always easy to do it, but it works the best. HOWEVER, the one thing you need to get better at any lick, or scale, or chord progression, or solo, is to get a metronome. Set it to a slow slow tempo and play your scale or chords on beat for set amount of repetitions, then speed up the beat very slightly, and repeat.
Keep going up in speed (with appropriate breaks in practice for concentration or fingers of course) until you can’t play the scale/chord cleanly. Clean means no buzzing ( or at least only very small amounts of buzz) and no mistakes. If you miss the fingering, slow the metronome up to a point you can play it correctly and master it there. In subsequent weeks, try to escalate the tempo again.
This works miracles for learning riffs and rhythms and scales and unfamiliar chords or picking patterns (jazzy stuff, etc). It will take a long time in the beginning. But the more you use the tool the better you get and the less time it takes to hardwire something in.
Also, when practicing scales, don’t just go up and down the scale all the time. In the beginning that may be all you can do, but after you can play them memorized, move them up and down the neck to different positions, and start doing the scale different ways–like by 3 steps up 1 step back, 4 steps up 1 step back, 5 steps up, etc. Or skip strings–play string 6, then string 4, then string 5, then 3, etc. The more ways you can get your fingers used to moving through the scale, the easier it is to memorize and apply later in a band or in new keys b/c your brain doesn’t freeze up when confronted by some new situation.
Lastly I recommend getting John Petrucci’s “Rock Discipline” DVD and maybe his book. There is no doubt in my mind that many of the exercises are beyond your abilities right now, but his way of planning and thinking and going about practicing is worth the dvd price and then some. Just concentrate on the general principles of variation. Besides it gives you something to shoot for in the future, and there are a number of good drills you CAN do, esp. the beginning ones in the booklet. He gives a huge number of tips on how to proceed–not just scales but finger stretching warmups, how to develop speed, etc. He’s the guitar equivalent to Thibs or Berardi–jsut like variety is king in training and eating, so it is in practice. And you can take his ideas and apply them to regular chords or scales. I can’t play a lot of the things he does, but just watching the DVD made me a better guitarist. I can’t say enough about it.
My number one key taken from Petrucci’s stuff is to do different things in practice–do warmups every time, do chords and basic scales every time, but then some days after you do the basic stuff try to learn a song instead of spending all the time on scales. Then other days spend your time working on speed, then other days spend your time working on new variations of scales or string skipping, or just generally making your fingers nimble. Makes practice more fun to vary things up.
FWIW, I’ve been playing guitar about 12 years.