Great read! One aspect that you may or may not have also written about is insulin resistance. 

Much like this article, the focus is always around cholesterol numbers, particle size, and inflammation markers. Insulin resistance is another marker to test that may be just as important or more important. If you are insulin sensitive, you know your body is metabolically healthy and all the systems should be functioning as they should. People who are pre-diabetic or diabetic have a difficult time repairing their bodies and LDL particles will knick the arterial walls which need to be repaired, this is where this oxidized LDL particles can enter the wall and begin the atherosclerosis process. If you are insulin sensitive, you body will repair itself before the plaque can build up. 

I am not a medical professional so my own research could be flawed and I may have been misled but since I discovered this as a potential root causes, I have focus on maintaining insulin sensitivity and inflammation above all else. And I have never felt better so YMMV