The endocrinologist should be able to test for other metabolic/endocrine conditions that could be a factor, with a higher cortisol level they may do tests for adrenal function. Also other hormone testing. It's good that although your cholesterol is higher, you have a good amount of the HDL, which probably puts you at less risk.
With your free T3 and T4 levels being what they are, you're certainly showing as hypothyroid. Whether or not this is related to the other labs, it's hard to say. When do you see the endo? They will likely want to get a clearer picture with further testing before deciding on a treatment plan.
The cold hands and low mood can definitely be due to your thyroid levels. Everything is so connected to everything else in our systems. I think you're definitely on the right track to getting some answers and having a plan of attack.
You're young, active, and it sounds like your doc is wanting to get the ball rolling. I know this doesn't help make you feel better, but there are many of us here that can understand!