I have a recurring thigh muscle problem which lays me off cycling for up to two weeks at a time every few months. (When it's at it's worst, I can't even walk). I've had loads of specialists looking into it over 10 years and 3 biopsies and they are still no nearer figuring out what the problem is.
Your situation is I'm sure very different as it sounds more like fatigue than pain, but my experience and research shows that there are so many things that can go wrong with muscles it's sometimes almost impossible to identify the cause.
Over the years though, and this might help you, I have found the following help ease my muscle pain and I suspect are quite generic aids to the problem:
1. Cherry Juice ( v. powerful anti- oxidant that helps clear out all the shite that muscles produce during excercise).
2. Creatine (you can get them in capsules but they are pricey)
3. Bio-Quinone Q10 (I have mine prescribed but I think you can buy it and it works a treat fo me.
4. Take magnesium and calcium tablets. Both are said to aid muscle pain and recovery.
Also, lay off too many fizzy drinks (prob. OK in moderation) as it's possible there's a link between the carbon wot's in'em and muscle pain.