There are a lot of misconceptions here, whether it's 1 mg 400 mg of testosterone injected, it will negatively effect fertility. HCG can keep the testicles producing small amount of T and E2, FSH injection can greatly improve sperm production when wanting to have.
Total estrogens is completely useless, I don't know why your doctor is testing for it, you want the sensitive estrogen test or LC/MS/MS test. It doesn't sound at all like you're working with somebody competent enough to manage your tear to protocol and I think that's why you're running into problems.