Angela, it is possible you are over hydrating. This will cause bloating of your tissues which includes the brain. For most of use there is little spare space within the skull for any expansion. This will cause a splitting headache
that will get progressively worse as the fluid is absorbed from the gut into the body. If this progresses too far the final result can be brain death. This is now the most common cause of death during organised runs nowadays. I am not aware of any deaths from dehydration by contrast (Dehydration - not heat stroke).
You are drinking a lot of water by any standards - at least twice what I consume on a warm summer day and much more than in winter. During a two hour bike ride at this time of year I might lose 300ml. Any more and I will be peeing all the time. While you will be pleasing the water and sports drink companies and many nutritionists who have been brainwashed by commercial interests, you only need to drink what you naturally lose during the day. I doubt you would be exercising more intensely than me or sweating more. There is no health benefit at all from drinking that much water.
When you say you are replacing electrolytes, I doubt more than a handful like sodium and potassium are being replaced. There are at least 20 minerals and then there are all the water soluble vitamins that are being flushed out by the deluge. The constant flushing of the gut dilutes the stomach acid and digestive enzymes. Along with this the digestive bacteria in the gut will be having a hard time surviving the constant tsunamis. This will lead to poor digestion and a consequent state of exhaustion due to malnutrition. This is common among women and athletes in general. You can see examples in the many articles I have published about the Hair Tissue Mineral Analysis.
The best course of action is to drink according to thirst (Yes, thirst is an effective measure of hydration - or lack of). If you are unsure of how much to drink then weigh yourself before a run and then again after. A kilo lost is a liter of water to be replaced - that and a little more.
You might want to get some Himalayan Sea Salt here and liberally salt all your food while avoiding processed salt. This will help ensure your electrolytes are restored, more or less. You can go a step further with a Hair Tissue Mineral Analysis. If this does not reduce the incidence and severity of your headaches, write me again.