Do you typically have pain in these locations when you have a migraine? Neck pain is a little alarming and I would be a little concerned because it's lasting so long.
You may want to see a neurologist. Any time the headache lasts a long time and doesn't respond to treatment you should be seen. Neurologists are much more knowledgable about migraines while other doc just tend to send you off with some imitrex (which isn't actually the wonder drug that it was supposed to be).
Hope you feel better.
I think I found out what it was last night, I think i'd trapped a nerve in my neck, I looked up the symptoms and found many many references to trapped neck nerves. I found these exercises and did them last night, and low and behold this morning I was fine! 
I started Vyvanse a few weeks ago, and went from 30mg to 50mg about a week ago, a couple of days after I started taking 50mg, I got a bad migrane which decided to stick with me on and off for 7 days today.
Now on day 4, I called my physch and she perscribed Imitrex for me which kind of worked on the Migrane but my shoulders and neck especially still really ached. Anyway I also stopped Vyvanse for a couple of days, the migrane still persisted though even not being on Vyvance, I then started Vyvanse again but dropped to 30mg for the next couple of days (the migrane was still lingering but not as bad as before). Now today my neck and left shoulder started hurting again, and also under my left ear is throbbing a bit, and my ear itself is throbbing a bit. I took some imitrex which seemed to help a bit but the throbbing is still there, especially at the back of my head (behind my ear).
Has anyone heard of anything like this before?, I don't know what to think. As it didn't stop when I stopped the Vyvanse for 2 days I'm not sure if it's even related.
Thanks
Steve