Hey, Tony! We have tutorials that cover the things you are asking about. But these things are sometimes in different places, mostly based on how in depth the material is. For example:

Originally Posted by: tonypal
My request is for a very structured series on applied theory for guitarists. It would go something like this:
1. Basics of theory (major, minor scales etc.)[/quote]
This is covered in the Guitar Fundamentals 2 course in the early chapters.

www.guitartricks.com/course.php?input=2

But the courses are designed to be concise & easy for beginners to work through. So, to go more in depth, you need to look in the catalog tutorials. For example, these tutorials go into much more depth about theory & scales.

http://www.guitartricks.com/tutorial.php?input=495
http://www.guitartricks.com/tutorial.php?input=453
http://www.guitartricks.com/tutorial.php?input=887
http://www.guitartricks.com/tutorial.php?input=835

Originally Posted by: tonypal
2. Identifying scale degrees; then, identifying positions on the neck. (similiar to Marty Schwartz'z covereage)
[/quote]
Again, covered in GF2, then much more in depth here:

http://www.guitartricks.com/tutorial.php?input=419
http://www.guitartricks.com/tutorial.php?input=898
http://www.guitartricks.com/tutorial.php?input=899
http://www.guitartricks.com/tutorial.php?input=462
http://www.guitartricks.com/tutorial.php?input=928
http://www.guitartricks.com/tutorial.php?input=929

Originally Posted by: tonypal
3. Building chords and then later, variations on chords and then alternative chord shapes
[/quote]
Basic chord theory is covered in GF2 & much more in depth here:

http://www.guitartricks.com/tutorial.php?input=148
http://www.guitartricks.com/tutorial.php?input=730
http://www.guitartricks.com/tutorial.php?input=731
http://www.guitartricks.com/tutorial.php?input=733
http://www.guitartricks.com/tutorial.php?input=734
[QUOTE=tonypal]
4. Ear training

The best way to practice this is to work on scales & chords systematically as well as songs! These systematic scale practice ideas are also good for ear training:

http://www.guitartricks.com/tutorial.php?input=451

[QUOTE=tonypal]
5. Timing..types, how to play using various timing.

6. Reading music (very applied with exercises)

These are also covered in GF 2 Chapter 4.
[QUOTE=tonypal]
7. Some simple to follow ways to write out song structures that enables us to keep correct time and structure.

That's a good idea that I'm not sure we've covered! I'll look around & see what I can find. I'll reply in this thread later.

Most of these things can be found organized in similar categories on my instructor page:

http://www.guitartricks.com/instructor.php?input=155014

Hope these links give you a place to start! Please ask more if necessary & let us know how it goes. Best of success!