Thanks for using the forum. I am happy to address your questions, and my answer will be based on the information you provided here. Please make sure you recognize that this forum is for educational purposes only, and it does not substitute for a formal office visit with your doctor.
Without the ability to examine you and obtain a history, I can not tell you what the exact cause of your symptoms is. However I will try to provide you with some useful information.
There are several causes of headaches. Headaches can be divided into primary and secondary. Primary headache disorders are headaches without a direct cause. These are diagnosed after secondary causes have been excluded. Secondary headache disorders are due to an underlying problem, there are many many causes but some include medication side effects, systemic illness, nervous system infection, tumors, bleeds in the brain or clots in the veins of the brain, and others. In the setting of a normal MRI and LP, a secondary headache disorder is unlikely.
It sounds like you have headaches related to neck discomfort. Causes of neck pain associated with headache include cervicogenic headache. Cervicogenic headache is a headache that is "referred" to the head from bony structures, muscles, and other soft tissue in the neck and shoulders. Symptoms are usually one-sided and include: precipitation of head pain by neck movement or awkward neck positions, head pain when external pressure is applied to the neck or occipital region, restricted range of motion of the neck, and neck, shoulder and arm pain. Treatment for cervicogenic headache includes physical therapy, medications including anti-inflammatories (NSAIDs such as ibuprofen), muscle relaxants, behavioral therapy, and other modalities.
In people older than the age of 55, one concern would be a headache due to temporal arteritis (also called giant cell arteritis) which is a disorder resulting from blood vessel inflammation. Symptoms include pain on chewing, yawning, etc. Vision changes may also occur and are serious. The diagnosis is made by a blood test called an ESR (sedimentation rate) and sometimes an ultrasound and/or biopsy. In people younger than 55 this diagnosis is exceedingly unlikely.
Lyme disease is very unlikely to be the cause of your headaches in the setting of a normal MRI and LP.
If you have not yet been evaluated by a headache specialist (a neurologist specialized in headache disorders) this may benefit you.
Thank you for this opportunity to answer your questions, I hope you find the information I have provided useful, good luck.