My goodness. This is a large topic. Also, though perhaps unintentional, there appears to be some hubris underlying your question. Before I continue to my answer, I want to address three points in your question:
1.) Regarding "quasi-tonalism" - extended tertian harmonies and the evolution into the 2nd Viennese School, Neo-Classicism (Prokofiev) and Neo-Romanticism (Ravel) should all be adequately covered by any legitimately accredited organization for higher learning. Please remember that you speak only from the view point of your personal experience of your one particular program; a program in which you were a minor and therefore spent less time there than the students who majored.
2.) Regarding counterpoint, did you study out of Fux? If that name is unfamiliar to you, then you absolutely cannot count yourself proficient.
3.) Regarding orchestration, it has nothing to do with how you feel but rather how the music sounded when you stood in front of an orchestra and conducted your own music or an arrangement of something. Confidence is one thing, but if it sounds like garbage, then it is garbage.
I'll preface my answer and say that it will not be comprehensive, but it will be enough to satisfy your question, I believe. Also, before I rattle off several avenues of music theory, I'd also like preface my answer by saying that even though a graduate student and an undergraduate student might be actually taking the same class, they aren't in fact taking the same class. Someone who has no experience writing music will approach an orchestration class much differently than someone who has extensively written. Orchestration, like many other aspects of composition pedagogy, is an art form unto itself. So even though it might seem like a lame answer, sometimes the most pronounced difference between undergrad and grad level course is time and individual experience.
Just to save us all a lot of time and headache, I'll list several avenues of graduate level and beyond music theory and highlight a couple. I'm not going to bother with resources - you can figure it out on your own.
In No Particular Order
- Lydian-Chromatic Concept
- Schenkerian Analysis
- Neo-Riemannian Theory
- Compositional Modeling
- Spectral Analysis
- Instrument Synthesization
- Assorted Seminar Classes on Analytical Histories of Specific Composers (In grad school I took a course on Beethoven that focused almost exclusively on his keyboard works. In seminar classes, you must also present your own analysis to the class in the same manner in which you might present a theory paper at a conference.)
- Carnatic Rhythms
- Electronic Composition
- Small Form / Large Form Composition
- Form & Analysis
- Pedagogy of Theory
- Various history classes
- Score Study & Analysis
I'd like to highlight a couple of things: 1.) Even though you asked about theory, I included the bit about history classes because I find I learn so much more about music theory (application, nuance, and language) when I learn more about the composer's life and the circumstances in which they wrote. Learning about composers is tremendously helpful. 2.) In compositional modeling, you create music by mimicing styles of other composers. It is a hands-on approach to learning theory and style. 3.) Electronic Composition may feature a variety of focuses. I have friends who focus on MAX/MSP. I have other friends who focus on musique concréte, and I have others who focus on synthesizing various instruments from pure waveforms. 4.) Schenkarian Analysis is an old warhorse of graduate-level theory. If you do nothing else from the list but want to feel like grad student (i.e. hate yourself) then study Schenker religiously.
As I mentioned, this list is not comprehensive. If I think of more later, I'll jot them down. Each bullet represents one class for one semester. Obviously there is more than a masters degree worth of work here. If anyone else thinks of something, they are welcome to add it.