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There are a few things that come to mind here...
Tension-type headaches can start with the type of feeligns you describe in your neck. You can read mroe about that in Tension-Type Headaches - The Basics.
Waking with this could mean a couple of things, both related to sleep...
1) Positioning or your pillow could be causing some neck problems.
2) Waking with a headache or Migraine is very often a sign of a sleep problem. Too much, too little, disrupted, and poor quality sleep are all strong potential triggers for headaches and Migraines. We have a video on this - Migraines, Headaches, and Sleep.
Flexeril is sometimes used for Migraine and headache prevention. The ibuprofen, on the other hand, should be limited to two or three days a week. If used more often, it can contribute to the problem by causing medication overuse headaches, aka rebound. You can find more information on this in Medication Overuse Headache - When the Remedy Backfires.
Everything I've mentioned are starting points, but only a doctor who can work with you in person can really answer your question. Hopefully the links I listed for you will give you some information to discuss with your doctor.
Was the neurologist you mentioned one you saw in the ER? If you've only been seen in the ER for this, the next step is to see your regular doctor. You really do need to get a confirmed diagnosis and work with a doctor on treatment to get this under control.
If your doctor isn't able to help you, it may well be time to consult a Migraine and headache specialist. It's important to note that neurologists aren't necessarily Migraine and headache specialists. Take a look at the article Migraine and Headache Specialists - What's So Special? If you need help finding a Migraine specialist, check our listing of Patient Recommended Migraine and Headache Specialists.
I hope this helps! Please keep me posted?