Absolutely! Your migraines can very well be due to your neck problems. I was in a MVA back in December and a few weeks after that I began getting migraines. I ended up seeing a neurologist that specialized in migraines, and he said that my migraines were probably due to whiplash, which is what I got in the accident. He said many people who have migraines don't even realize it stems in their neck.
I will tell you from my personal experience, don't give up too easily! I have been to physical therapy, chiropractor, and massage therapy. I have been on multiple medications, and have had two series of cortisone epidural injections, a cervical rhizotomy, and trigger point injections. The point I am making is that there can be help out there to help you get better or at least be able to cope with the pain better. You shouldn't have to just deal with the pain. The Pain Management Doctor can help you. If the migraines are from the neck, he can help you with that. There are many things you can try and do to cope.
I can't answer what the long term effects are, but I know it does get old. I am on 11 months of pain, mostly everyday non-stop. It does take a toll on life as you begin to pull away from life due to the pain. Depression can set in. The most important thing is to not let it take over your life. It is easier said than done, but you have got to maintain a positive attitude and not let it beat you. Good luck!