Let's get this disclaimer out of the way: I'm not a dietician, doctor, or any kind of medical professional. I'm simply a college student who has lately been busting her butt trying to be healthier and yet am still not seeing results. I've been feeling worse now than I did when I was eating junk food. It can be really discouraging to not understand why your body is going against you instead of responding well to the healthier habits. I just thought that I could give some helpful ideas of easy things to do to keep your physical (and mental!) health in check so that this "I'm still feeling blah" doesn't drive you crazy.
First thing's first, I'd go see your doctor. I guess I should say a doctor, because it depends on what your specific issue is. If you think it's more of a flu or general fatigue, even your school health center could help. If it's stomach issues or aches and pains, then maybe your primary care doctor or a specialist can help. That's what I ended up having to do: I actually went to my PC doctor and then to a dietician to get some advice.
The next thing I would try to do is to not give yourself a hard time. Your body is trying its best to keep you healthy, alert and strong, so just try to return the favor. You don't have to overhaul your whole life: just do the little things. More water, less processed stuff. More veggies, less fried foods, you know? Also: get more sleep. I'm still trying to work on that one, but at least aim for 8 hours (9-10 hours if you're feeling especially exhausted).
I'd also probably do a little research depending on what your doctor(s) said. Like for me, one of the possibilities for my constant headaches, GI issues and muscle aches could be a gluten sensitivity. So, in order to check on that, I'm going to need to change up what I eat for a little bit. I've been looking at gluten-free ideas, or at least at good carbs to eat (like rice for example) so that I don't eliminate carbohydrates completely from my diet (because that's no good for anyone). So if you've been exhausted all the time or having a cold, maybe look up some ways to get more sleep, or see if you can find some more information on your symptoms. Obviously a doctor or other medical professional is the best route, but a little Googling can help put you at ease (just don't WebMD yourself into a panic attack).
Oh, and try to remember that you will feel better: no matter if it's allergies, the flu, or a total mystery as to what's throwing you off. You can tough this out. Just give it some time (and patience).