Muscle atrophy after illness

Due to a lengthy illness, I have experienced disuse muscle atrophy. My recovery is complete enough that I can walk around and yesterday I even ran nearly a mile, but I need more than physical therapy to rebuild what's been lost, mostly in my arms and legs. I didn't realize how fraile I looked until someone took a photo of me today, and I was horrified.

I went to the grocery store tonight and bought Muscletech Elite 30g protein per scoop along with lots of egg and dairy items and several cans of tuna. This is just to get me started until I know what I'm supposed to be doing and can shop accordingly.

I found calculations to figure out how much protein I need, but they vary and none take into account my current state of atrophy. Maybe someone can look at my numbers and tell me which calculation is best for me? Other than physical therapy 3x a week, I'm mostly sedentary.

5' 7.5"
140 pounds
51.8 pounds of body fat

I can't even lift my own body weight from a deep squat. I tried and fell over. It was embarassing because people rushed over to help me. The bar had no weights on it at all, I just couldn't didn't have the strength to stand up.

One last thing - My PT is a man and I'm a little shy about asking about when we can start glute therapy and exercises. My buttocks have become so limp and flat that instead of one crease between cheek and thigh, I have 4 or 5 going down the top of my thigh back there like an old lady. I lost 25 lbs while bedridden, mostly muscle due to lack of movement.