Struggle to gain weight

Hi, I am having troubles to gain weight. As some people on this forum. I read through some threads but they did not seem to describe my symptoms.

I started the gym 5 months ago and at first had okay progress WITHOUT any noticeable mass gain though. I made sure that my calories are on par with calculator readings: 3.23k in my case a day for clean bulk. Unfortunately, it did not seem to help with hard training and enough food.

Now, as probably others having similar issues, I started to look into medical problems. The symptoms I have are: it seems like I cannot absorb fats very well, I always eat around 50g of nuts and a protein shake before going to bed and I have yellowish stool if I do not eat much fiber like vegetables etc. If I do eat enough of them, the color is normal. Also, another troubling problem is nightly wake up between 1-3 am which would indicate liver time. I was skinny since teenage years and both of my parents were as well. Now both of them have some solid weight on them and are not skinny in their 40s.

My reasoning is that I might suffer from lack of sleep because I find it hard to get back to sleep after those wakeups. I went for a blood test to rule out diabetes and similar problems. Tests indicated normal fasting blood Sugar and thyroid hormones.

Stuff I eat: organic meat like venison and beef, organic veggies, eggs, nuts, fats like coconut oil and some animal fats, avocadoes. My diet is kind of paleo-ish since I do not like grains therefore I don't consume them. Not saying that paleo is good in my situation. I cook all my food, eat soups made of vegetables, I only eat spinach and tomatoes salads raw, all other veggies are cooked.

Finally, I have persistent Acne since 14 years old that does not disappear and feel a lot of mental fog. Also, I do not feel rested in the morning, probably due to bad sleep.

I take 600 mg of magnesium, caprylic acid and olive leaf extract. That's all.

Anyone has thoughts?