It took me a long time to get over Lyme disease after not being properly diagnosed initially. I would recommend looking into the work of Stephen Buhner. He just released a new book called Healing Lyme 2nd edition, and wrote several other books for Lyme disease co infections, as well as one titled Herbal Antibiotics, and Herbal Anti Virals. His site is Buhner Healing Lyme dot com too, good info there.
The most important thing though, is whatever you are dealing with. It will take some time to get well, and you have to be more careful then someone healthier in pushing yourself. Eventually though startling low and slow with a new strength training program will help boost your testosterone again, as well as help dealing with de conditioning. Cardiovascular exercise is usually harder on the system returning from illness, as opposed to resistance training, so be extra cautious with that as well. The herbs really do help and are broad spectrum enough to cover viral, bacterial, and fungal infections, depending on the types you take. Buhner's books discuss all of this including types of herbs, dosages, side effects, interactions, etc. Good luck, doesn't sound like anything that will keep you out of the game too long.