Hey Matt,
Chronic headaches I know can be a debilitating problem and sometimes very frustrating to find a specific etiology. I have read before that as many as 40% of ED evaluations for acute headaches the patients are discharged without a cause identified. Even when a diagnosis is rendered many forms can only be managed not cured, per se. I would focus your attention more on general causes of the headache rather than testosterone.

Neurologists divide the headaches generally into two groups- the primary headaches- including migraines, tension, and cluster headaches. There are different theories about why they happen but nothing is rock solid proven. Once one of these diagnoses are made then certain treatments are offered. Alot of times the doctor will guide you to identify the triggers for these headaches, to avoid them and to pick up signs the headache is starting to abort it before it gets out of control. As you might have been told and experienced, narcotics have a limited role because a tolerance develops fast which limits their effectiveness long term. The most common useful treatments are mixtures of caffeine and aspirin type ant-inflammatory drugs.

The second major class of headaches are the "secondary" types- which are headache pain caused by another systemic or local disease process that leads to the pain. There are a handful of these that sometimes may not be recognized initially that are readily treatable when picked up on. Chronic sinus problems can be overlooked. Temporal arteritis- usually older folks- gives really bad lateralized in the temple headaches. A simple test called a sedimentation rate or ESR can suggest the problem.

Although this article is dated (2001) its a great review paper for the primary doctor's approach to chronic headache patient. I hope you get control of your problem.

http://www.aafp.org/afp/2001/0215/p685.html

You may need an MRI as the guy said below, you could have a problem with your pituitary or something else, make sure you've got a good doc.

In my experience, no they won't go away but I do believe the intensity of mine decrease a bit when I'm running test. For example, they use to get so bad I would start puking and I just would not be able to stop. Couldn't hold any fluid or anything down and I'd have to go to the emergency room to get something for pain and dehydration. When I'm on cycle and get one, most of the time I'll be able to take my meds and keep them down without puking. Of course I'm still out of commission and have to lay down for several hours but that's way better than puking and not being able to stop.

Your doc is putting you on trt with serum levels in the 400s?