Thanks again, JTE, for taking the time to explain all of this.
Expanding this, especially point 1, is the crux of the recent discussions. When I say "Learn the major scale and how it's constructed", I do NOT mean "be able to wiggle your fingers to the right spots to play a major scale". For this, "knowing" the major scale means:
A. You know its construction- W W H W W W H
B. You know how to determine the correct notes (with the correct enharmonics- it DOES matter) for the scale in any key. That is, you know how to figure out that A major is A B C# D E F# G# A, and you know WHY it's F# and not Gb.
C. You know what it sounds like.
D. You can find the notes for it and play it across the neck starting in any position (not necessarily starting on the root- this is vital for actually playing music instead of playing scales), and you can find the correct notes and figure out a fingering across at least two whole octaves to get from the first fret to the 12th.
Only then do you KNOW the scale. And the diatonic major scale is the first one to learn like this. In fact, you could a long way with that being the only one you know.
Ok. I think I'm on the right track with this, but I'm at the very start. I know a few patterns to play the major scale, and I number the notes when I play them (1-8). Because of this, I know where 1, 3 and 5 are, so it helps me to identify the right notes for a triad, and for a 7th and the octave. For me, right now, this is the bridge between scales and chords.
A - I do know the construction pattern of whole and half-steps. It actually falls in line with the patterns that I've been practicing, so I hope that this is the right way to bind the physical playing with the mental awareness of why I'm reaching for particular points on the fretboard.
B - Physically, I think I'm doing this. I practice scales backward and forward... I haven't done any starting from the middle yet, but I'll try to mix it up and see how much it throws me off.
A problem for me here is that I don't know the notes by name yet. I can figure them out when I'm playing, but I need to start on an open string, or on the 12th fret and count out note names right now to know what note I'm playing when I hold any given fret. Once I have that root note, I'm able to (somewhat slowly) name the other notes in the scale though.
I do know a little about enharmonic equivalents... that's when a note has one name going up the fretboard or scale and another name going down. Its generally the sharps and flats, from what I understand, but I've seen (from discussions on TalkBass) that later on, there are other rules that complicate this. I don't have a grasp on those yet.
C - I'm working on.

I can tell what a scale sounds like, and I can tell what a triad sounds like, but if you just pick a note in a scale (or anywhere on the bass for that matter) and play it, I can't identify it yet. If I hunt around, I can find the same note, but it takes some experimenting still.
D - I still rely on the patterns for this. I'm not sure if I'm able to start in the middle of a scale and play the rest either backward or forward, because I haven't tried. I'll do that though. I've also not learned how to play any of them for more than one octave. I think I can figure that out if I sit down and just apply WWHWWWH to whatever note I end on and see if I can recognize any patterns from it. I'll try that as well (and then look around on line and in my books to see how far off I am).
For point 2 (Learn how basic chords are built from the major scale- e.g Major is 1,3,5, minor is 1,b3, 5, etc.). This is covered in any basic harmony book. The goal is to be able to figure out for yourself (that is, no book or chart or diagram) the notes to the main types of chords. I think you should at least be able to spell out:
A. Triads- major, minor, diminished, augmented
B. 7th chords- Major 7, Dominant 7, Minor 7, Minor 7b5 (a/k/a "half-diminished"), and diminished.
In order to be able to do this for any chord, you need to know the correct notes in the major scale. So, instead of trying to memorize that an Abmin7 is Ab Cb Eb Gb, just build your knowledge- You know that the major scale is W W H W W W H. Start on Ab (the root) so the whole step is Bb, the next whole step is C (the third), half-step to Db, whole to Eb (the fifth), whole to F, whole to G (the 7). And from knowing that a minor 7 is 1, b3, 5, b7, you pull Ab, Cb (not B), Db, and Gb.
I think I understand how chords are built for the major and minor scales. I've been practicing triads and sometimes 5ths and 7ths (or 5ths with octave, which I like the sound of better than 7th right now) directly after practicing scales. This is mostly for muscle memory.
A - I can identify the right frets, physically, but it takes me a few seconds to name the notes, and, I need to know the root to do it. I can play major and minor chords, but I've not practiced augmented or diminished yet. I saw them in Bass Guitar for Dummies, but I didn't want to go there until I felt that the first 2 were locked into my head.
B - Like above, I can do 7ths for the major and minor, but haven't approached the others yet. I think that I'm going to have to learn the augmented and diminished patterns and their sound before I try. I don't want to confuse them with the major or minor.
For the rest here, I'm still working on identifying the notes on the fretboard.
3. Learn the Harmonized scale- write out the scale on paper. Using C as the example, you'll get:
C D E F G A B C
I'm not up to this point yet, but now I do seem to have a roadmap to follow. I've actually not heard of the Harmonized scale until now. I'll read up on that later.
And a lot of this is stuff you can do on the bus, during pointless meetings, and in your head when your wife is telling you about those new shoes....
I can tell this is real-world experience... I actually do this, and she knows when I've zoned out. She breaks my focus when she starts talking about food though.
I'm going to work on the above so that I can get to the rest of what you said... this is a lot of material, and its only the first 3 points.
That's enough of the 8 points for now, but I want to leave you with this too.
SING everything you play. Playing music is about sound, not physical location. If you sing everything you practice (even if you sing like me- a friend described my vocal ability as "a duet with Yoko Ono and Linda McCartney") then every move your fingers make has a sound associated with it. So when you hear that Amin arpeggio in "Badge" your ear tells your fingers what it might be. So when you hear something similar in another song, you have a head start on finding it.
John
I'll try this... I get a bit self-conscious though, so it probably won't be a regular practice for a while. And, sorry to everyone else. I didn't realize how lengthy that reply was until I saw the preview.