I Don't Know How I Should Feel or What to Do

Any other labs?
Like lipids, metabolic panel, CBC? Metabolic panel checks liver , kidney .

The pituitary MRI the radiologist will view your entire Brain. So no worries.

Read up on Cushing. And other labs to confirm if you have that. Good that she is concerned about adrenal functions.

You may want to fix that first.
Thyroid I would not worry. Your TSH is fine. No reason to think there is something wrong their when you have low t and low e2 causing your symptoms.

After the diagnostic tests and adrenal stuff, if she gives you testosterone at least get 200 mg every 2 weeks and you can inject more often on your own.

You really need to check prolactin level as well.

Your LH and FSH low probably secondary hypogonadism. If you having baby soon you can try clomid instead of testosterone and HCG. Clomid will keep you fertile.