You're training regularly and eating healthy, feeling great majority of the time, and we do what we can do avoid illness, however, our bodies are not impenetrable. It does happen. Illness, injury, tiredness happen and may mean you may not always feel up to training, or have to take time off.
If you feel unwell, the severity of whatever your illness is, should determine whether you train or not. If your symptoms are minor, just a cold, allergies, light training may be okay, however, if symptoms are severe and below the neck you may want to take off. But the main thing is to listen to your body. Not to mention, you don't want to infect anyone else. When in doubt play it safe. You won't lose gains overnight, and a break from exercise could speed up recovery.
Aches and pains are apart of living an active normal lifestyle. Working out should make you feel better and they should ease up when training properly. However, if they persist, avoid types of exercises that make them feel much worse. Try lower weights with higher reps, train slightly around pain, try to perfect form. Make sure to get checked by a professional if you experience long-term serious pain.
Tiredness got you down? If you are serious about training, make sure to make sleep a priority. If you suffer from disrupted sleep, that could impair your training. So focus on getting a solid nights sleeps, incorporating good nutrition and recovery. And if you are sleeping well, but just need a boost before your workout, try a small bit of caffeine or an all natural pre workout to boost your training session.
Overall, be in tune with your body. You want to train well, train effectively and at your best for optimal results!