I started writing about physical exercise and noticed that you get enough of that and still fill physically tired. You also seem to have reasonable food and sleep habits.
I'd say, there is not enough information to give you the solution, but I'll throw in some ideas, and you can check if anything resonates.
Can it be a problem with information overload? Reading too much, or Internet surfing can drain a lot of energy. It may feel as if you are physically tired, but it is a false feeling. Usually, daytime naps help with this. You process the avalanche of new info and feel refreshed. Try it, if it works, you have a suspect.
Can it be that you do not rest enough? Overtraining can happen to enthusiastic guys. Especially if you run every day.
How about personal life? Are you in love? You don't have to answer, just think about it. Heart matters are the huge drainers.
Also, you mention a few days a month when you do feel enough energy. Try to do a comparison of these days with the usual low energy days.
Look out for locations, routine, activities, people you meet, what you do the day before etc. Are there any consistent patterns?
Did you have high energy levels in the past? If you did, when did it change, what was the main factor?
This is all I can suggest right now. I did have the problem of low energy, but by the time I exercised like you and ate healthily, it all gone.
Oh, last idea. If you do not already, try "listening to you body". Is there any desires or cravings that you suppress? Do you want a particular cheat meal or something. You seem to be in control, and disciplined. At this stage, you body can give you valuable advice and you should follow it, even if it goes against your regimen. If you try to tough it out, the body sometimes goes silent and doesn't let you know what's wrong. Your "WTF" description matches this situation.
Hope some of these ideas will help you to figure out what's going on.
Good Luck.
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