If you cycle less distance i.e. go back a few months, do you still get this. If no, perhaps you are still adapting. As said, 8 miles a few times a week to 50 at the wknd is a big step up, perhaps too much. I might think about reducing my wknd distance and increasing the weekday distance. Extend your commute home in the summer (nearly) evenings and/or increase your frequency. A few weeks of that will give you some answers.
The other thing that occurs to me is your bike setup, that could certainly cause headaches and general fatigue. Wrong height handlebars or wrong length stem will increase strain on your neck and shoulders which might trigger the headaches is one example.