I agree that Prozac could be causing your discomfort. This is based on my experience with the drug. As anxiety was my core problem, and sounds as tho' it is yours, my non-medical opinion is that your doctor may want to consider another less stimulating antidepressant.
When I was on Prozac, I stayed awake night after night; had all the aches and pains you mentioned. It was not the right med for me. All systems are different, and many people do just fine on it.
Best luck.
First question: are you feeling better anxiety wise? You never mentioned that. That has a lot to do with how to approach side effects. Fatigue is very common with meds; in fact, when they work to relax people they are quite often sedating to some extent. This will often pass, though everyone is different. Muscle aches are quite common with meds as well, probably because they tend to interfere with magnesium absorption and because they target neurotransmitters that don't just help regulate brain function, they also regulate other things. Serotonin also helps relax muscles and helps the digestive system work and relaxes blood vessels, so when you alter serotonin function, as Prozac does, you can alter all these other things as well. But if the med works really well, you tend to be able to live with this stuff much better than when the med doesn't work well.
It could be your anxiety or your medication, contact you doctor and let him know how you are feeling. Take care.