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If you're serious and you really want to become a better player... The Advancing Guitarist by Mick Goodrick
https://www.amazon.com/dp/0881885894/
But fair warning... he doesn't go easy on you. He assumes you're ready to take practicing seriously and he gives you assignments that are intellectually and physically difficult.
However, if you are serious and willing to put in the time and effort this book can offer so much.
Harmony 3 is more chord scale considerations, modulations, diminished harmony, and an expansion on modal interchange. Harmony 4 is mostly modal harmony. It's also worth noting that the Berklee books are DEFINITELY geared towards jazz harmony. If you want the more traditional harmony, I recommend Tonal Harmony by Kotska and Payne.
As for the other Berklee books, I would heavily recommend Mick Goodrick's Advancing Guitarist. Modern Jazz Voicings is pretty cool, and Arranging for Large Jazz Ensemble probably assumes a very high level of knowledge of arranging techniques from the get go. Essential songwriter I have no experience with, but I know some friends who really enjoy the Berklee book on lyric writing (can't think of the title). Music notation is about writing music by hand and can be useful if you aren't familiar with a lot of written notation (but seeing as you are a BoCo student, I assume you read.) Rick Peckham's Jazz Guitar Techniques : Modal Voicings seems really good, because he is a beast teacher/player.
Jazz is definitely one of my interests, but I tend to lean in a Fusion/rock/funk direction most of the time.
For all intermediate to advanced guitarists: The Advancing Guitarist by Mick Goodrick.
I can't even really describe it. It's like he describes ways of exploring the Guitar as an instrument of one's soul the way a Zen master might lead one to enlightenment. Truly profound, fun to read and explore the ideas on the guitar, and possibly life changing if guitar is important to you. Highly recommended for any advancing guitarists out there.
Playing on one string helps break things up. For more on this approach check out The Advancing Guitarist, which boils down to this:
Spend a good amount time practicing scales and chords on each string, then combine 2 adjacent strings (ex. A and D, then G and B), then 3 adjacent strings etc.
As far as a routine for learning songs and relevant theory it doesn't get much better than this.
Thinking about your original post more this might not be the book you're looking for.
For straight up the best in guitar theory I'd recommend:
https://www.amazon.com/Advancing-Guitarist-Mick-Goodrick/dp/0881885894
This is the book all the guitarists went nuts over while I was at Berklee.
Even before that I would suggest Effortless Mastery: http://kennywerner.com/effortless-mastery
This book is essential for anyone getting serious into playing music and looking into theory.
In lieu of a big spiel, buy this book.
Hell yeah. There is a reason why a lot of metal guitarists also get into jazz (eg, Marty Friedman).
Here are my recommendations:
You'll need to learn how to read musical notation for this, but it's worth it.
Victor Wooten: Groove Workshop
It's a bass video and it's not even about technique, in particular. But it's filled with incredibly insightful advice for musicians of any kind. Highly recommended.
Mick Goodrick - The Advancing Guitarist is well worth the outlay and will take you a good while to work through.
I've seen someone recommend this, and it looks pretty good. And I'll go ahead and throw some Ted Greene out there.
The Advancing Guitarist by Mick Goodrick