What Causes Intermittent Headaches Along With Itching And Watering In Eyes?

I was diagnosed with Lyme disease in September after having a tick bite in July (blood test ) I had no rash but had flu like symptoms which promted me to be tested . I took Doxy for 21 days but since then I have had a headache every day off and on and usually worse at night (more in the back of head and neck but also moves around ) Now I have developed some type of infection in my eye itchy red watery sensitive to light I have used eye drops the itching is better but it still runs and is red and feels irritated . My MD thinks Lyme is gone after antibiotics but I feel like I still have it I also gt body aching and vrious pains all over that come and go What should I do and How do I know if it is Lyme or something else ?