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.
While I can not view your CT to confirm that you do have a basal ganglia calcification, I will reassure you that if this is infact the fidning on your CT that a calcification in the basal ganglia is a benign finding. There are some theories as to why people get these calcifications but it is not entirely clear. What is known for sure is that they if they appear to truly be calcification, and are just small/minor, they are of no clinical consequence. They are VERY common. A small calcification in your basal ganglia would not explain your headaches, and is not concerning at all.
In treating chronic headaches such as in yourself, the treatment should include two types of medications: preventative therapy and abortive therapy. Preventative therapy is a medication that would be taken every day regardless of whether or not a headache is prevent. This type of medication is used to prevent headaches from occurring, and there are several types including but not limited to beta blockers such as propranolol, calcium channel blockers such as verapamil, and others including topamax, depakote, elavil, etc. A lot of these medications were invented for other uses and are used not only for headache but also epilepsy and depression. They have proven very effective in preventing headaches. The second medication is abortive, meaning it is used when a headache is coming on. The medication used depends on the nature of a headache. If it is a migraine type headache, a group of medications called triptans can be used. And so on. However, with frequent use of abortive medications including triptans, tylenol, advil, and others, medication overuse headache occurs. The medications being used to treat your headaches start to cause your headaches! This requires a specific treatment in which the over-used medications are slowly stopped and replaced with more long-acting medications. Tylenol with caffiene, and similar medications, can cause medication overuse headache if used too frequently. Lyrica, which is used for fibromyalgia, can be used for chronic headaches too.
The combination of amitryptiline with topamax is not dangerous in the vast majority of patients. In fact, this is a very commonly used combination. There are of course very rare people who have a reaction when both medications are combined, so the manufacturer is obliged to put this on the drug insert. The important thing in starting combinations of medications is simply to keep an eye out for side effects or potential complications, but avoiding some combinations all together because of rare risk of an interaction is not always necessary. Certain medications are contraindicated in combination, they should NEVER be given together, but amitryptiline and topamax are not in this class.
When you see your physician regarding headaches, the important thing is to lay out a plan, try some abortive therapies (if zomig is not working, another triptan may) and then find one or more maintainence therapies that work. unfortunately, sometimes it is a matter of trial and error to find the best combination, as one patient differs from another in terms of what works.
You mention anxiety and depression, which can of course cause a lot of sufferring but also significantly contribute to headaches. So I recommend you share these symptoms with your doctor as well, so that the appropriate therapies can be started for these too. Sometimes, the same medication can target both symptoms. For example, amitryptiline at specific doses can be used both as an antidepressant and a headache treatment.
Sleeping well and exercise are also important for headaches. If you do not sleep well, make sure to discuss this symptom with your neurologist as well.
If after several evaluations by a regular neurologist your headaches are not yet controlled, evaluation by a headache specialist (a neurologist specialized in headache medicine) may be beneficial to you.
Thank you for this opportunity to answer your questions, I hope you find the information I have provided useful, good luck.