Lisa has done a wonderful job at answering your questions today...I will just chime in with my personal opinion and some on-line research I did to try to give you even more information.
I went through this too...wondering if this could be something else. But I am thinking that while misdiagnoses happen...I think it is more rare than not. Did they do a battery of blood tests for you at first? I know they did with me. What does your doctor say about your concerns that it could be something else like Lyme's disease? What specifically made you think it could be that instead of MS? I suppose your doc could test you if you were very worried. But after all this time has passed I am going to make an uneducated guess that it probably isn't Lyme Disease.
I am not a doctor, however, and so I will give you some more information from folks who are wondering the same thing.
Here is a personal blog of a man named Erik who has been going through the process of determining whether he has MS, Lymes Disease, or both.
Then I also found an article written by a woman named April Clark, who talks about her attempts at figuring out what is medically going on for her. Here is an interesting quote from that article:
"Lyme disease creates lesions on the brain like multiple sclerosis (she was diagnosed with MS at 19), and it's this epidemic that's totally misdiagnosed and under diagnosed," Stevenson said. "I've been tested twice before for Lyme and it was negative. It takes an average of two years of symptoms to diagnose. I'm just going to follow what the doctor has to say and probably undergo long-course therapy of antibiotics."
And finally...here is a long thread based upon a question similar to yours about the differences between Lyme Disease and Multiple Sclerosis.
There are so many rabbit holes that you can potentially explore, but I would begin first by presenting your concerns to your doctor so that he or she can either ease your mind or begin to act upon your concerns.
This was a very intriguing question. Thank you for asking it. I wish you all the best.