After I contracted lyme my case went "dormant" in my body. I didn't have aches and pains until 5 years later. I was sick for a week after the bite and after that I really only had strange eye problems, ex: sunlight seemed bright, jumpy vision. Eye issues went away a couple weeks later. I would say I didn't notice much of anything for many years. I also have severe stomach issues, actually ended up with IBS. Stomach issues started gradually, and got worse later. There's a good documentary called "Under Our Skin." I've heart it's on netflix and also on Hulu. You can also see clips on http://www.underourskin.com.
It's worth taking a second look.