What is your height, weight and gender?
I think low HDL and low Vitamin D is indicative of dysbosis and/or leaky gut. So you might just need to keep at it longer, increase the vitamin d and heal your gut.
In terms of cholesterol, you can drop your sat fat intake and your LDL will drop. IDK if you actually need to do that or worry about it, but it's something you can do to make your results "better." But you might just want to eat until satiety at each meal and stop snacking.
Are you purposefully restricting calories? I would be starving if I only at ~1150 calories a day.
Poke it quickly, with a stick.