I'm not a doctor (which means you may like me lol), but it sounds like a migraine to me.
That said, call your doctor and explain your fears. Tell her that you're worried about meningitis or a blood clot - and these are valid fears.
Try one dose of the flexeril. It will likely do nothing, or very little, but you need to be able to say you were treatment compliant and treatment failed. Since the pain is bad at the base of your skull, I wonder if the muscles are tight there. The flexeril might help.
If you can take it, try an excedrin migraine instead of the ibuprofen, but make sure there's been enough time in between doses. If you take the ibuprofen every 6 hours, wait 6 hours after the ibuprofen to take the excedrin.
Change your pillow. Since it's really bad in the morning and when you lay down, try another pillow, preferably a new, hypoallergenic one. I'm not saying your pillow is causing it, but it might be making it worse.
If you have a heating pad, put it against the back of your neck. Get those muscles loose. Better, if you can get any Bio Freeze spray or Icy Hot spray, spray it on the back of your neck where it hurts the most. I prefer Bio Freeze because it smells far less, but some prefer Icy Hot.
These are all symptom relievers. They won't cure a headache if it's caused by something else.
In the meantime, definitely call your doctor back and let them know your symptoms are not gone, and follow up on the MRI, and talk about your concerns. They are real and valid.
And I'm with you - I hate the way ER docs treat migraines, though I do understand what they are going through right now.
Let us know what happens.