Sorry for the delay, I'll answer all your questions now.
1) I was having symptoms, no energy, low motivation, hard time building muscle, put on fat way too easily, no hair anywhere, no morning wood, low libido, decreased bone density as verified by a bone density scan. It wasn't further investigated because I was 16 and my endo said I'm probably just a late bloomer (my dad was).
2) At 16 I got an MRI of my pituitary/brain and everything was fine, except for the fact that my pituitary itself was much smaller than normal.
3) In terms of labs and other body systems... My morning cortisol was tested to be normal, but in the high end of the normal range (blood sample, not salivary). My TSH has always hovered a little high, around 3.1-3.9. Now before you say "you're hypothyroid", my free T4, free T3, reverse T3, antithyroid antibodies, have always been normal, and I have no symptoms of low thyroid. In fact, I have HEAT intolerance, lol.
4) My mom is into functional medicine and has always attacked me in that approach. I take plenty of vitamin D, fish oils, a good bioactive multi, etc... Oh and my DHEA levels has always been very good.
By the way, I ditched my original doctor (the endo that has been following everything), because when he decided to put me on testosterone, his only protocol was for him to do a 400mg injection once a month. I walked out the door when he said that. I'm now seeing a VERY good urologist who is treating me.
Follow up: He currently has me on 60mg test cyp e3d. He had me put sperm in a cryobank just in case a clomid/hcg restart doesn't work in the future. At the moment, no AI or HCG, he says he'll add those in if needed. I feel great since switching from the testim to the test cyp. I don't know why but I have loads of energy, morning wood, finally horny, and oily skin. I think my skin was absorbing the testim too fast, causing a spike a few hours after application and a very low trough for most of the day.
Hope that answers all your questions.