Your HDL going up is definitely a good sign! As for the rest, it's possible that you're just genetically predisposed to high cholesterol regardless of diet, which is what appears to be my problem:
A full NMR or VAP lipoprofile can determine your actual particle size and density so you have a better idea of what's going on. Also, Dr. Davis at HeartScanBlog is very big on niacin:
Give me a friendly Christian any day over an asshole atheist.