Hi Joe -
One thing that has really helped me "put it all together" is practicing a tune using the following routine:
1) Figure out how to play the chord changes in five "master positions". When working in a position, do not leave that position on the neck...figure out a voicing for each chord in the progression without leaving that position.
2)Now do the same with the melody.
3)Now do the same with the arpeggios for each chord.
4)Now do the same with the scales for each chord
5)Now limit yourself to a rhythmic duration (like a quarter note) and play each arpeggio for each chord without leaving a position and try to "link" them together. Just go for the closest available note as you change chords/arpeggios. Again, it's important that you do this without leaving the current position you are working in.
6) Now do the same thing with the scales.
Usually by this point I have memorized the changes to the tune and I am able to start combining scales, arpeggios, and positions. I keep doing this process until it becomes more and more comfortable, and eventually I start to see the whole neck when playing over the changes. I start to incorporate chromatics, too.
Limiting yourself to eigth notes when trying to improvise is a good exercise, too...the idea is just keep playing eigth notes no matter what..don't stop, even if you hit a wrong note.
Here is a small of what I mean over the first four chords of "All the Things You Are" (a tune that always gave me trouble until I used the above method):
Chords (1st position)
Arpeggios (1st position)
Arpeggios linked (lst position, 1/4 notes)
At this point you should be hearing the chord changes reflected in the line (and you can use this as a lick over those first four bars of course). I can't map out the entire process here in this message, but here is a sample line over those first four bars. After working out the chords, arpeggios, scales, and chromatics over those first four chords, you might end up with an 1/8 note line like this:
sorry if this message is a little unclear... am rushing thru it at work! I hope you find it helpful!