Lots of things could be happening here.
Could be over training, you’ve only recently started back, ease into it…it’ll come in its own time, if I’ve had a lay off I’ll only run a mile or so when starting over again.
Depleted/low sugars post exercise…don’t go overboard but follow exercise with a small shake or meal consisting of carbs, protein and fat….then about an hour later do the same again, small though!
Bring your water back down to 3 litres a day, see how you feel.
Mix things up, are you doing any weights?…people get obsessed with cardio when trying to lose weight and hammer themselves into painful joints, fatigue etc….go easy and fit some weights in there too.
May also be getting the headaches from the carb reduction in the same way people who cut out coffee get headaches, think withdrawal but not as dramatic as drugs obviously!
It looks like you’ve put in place loads of good lifestyle changes but done them all at once and potentially to an extreme for you.
Try some of the above and see how you get on.